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How did the first self replicating organism come into existence?

How did the first self replicating organism come into existence?


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When people try to explain evolution, they tell me that evolution is a cumulative result of mutations & natural section of the more superior individuals of a particular species. I think I'm fairly convinced with this explanation.

But when I think about it, all of them assume that there was an organism, however simple, that was capable of self replication & occasionally mutate. How did such an organism come into existence? Can anyone explain this?

An answer I found on Reddit didn't really convince me.


Evolution or (as Darwin called it) "descent with modification" is a theory which explains the origin of the species NOT the origin of life. How the first life arose is completely irrelevant to the theory of evolution. What evolution does explain is how and why we have such variety of life on earth all descending from the same organism.

What you're asking about is not a theory of "evolution" but rather a theory of "abiogenesis." Although there are many interesting hypothesis for how abiogenesis happened (e.g. the RNA world, the "metabolism first" theory, etc.), the fact is we simply do not know yet how life first arose. What we do know is that life first arose between 3.5 and 3.9 billion years ago. That's a really long time ago compared to lots of other important events in natural history (even the Cambrian explosion where modern animal phyla evolved was only half a billion years ago), and so it shouldn't be surprising that it's a hard problem.


We don't know how self-replicating molecules first arose (and probably never will know exactly) but the Earth is large and had 500 million years (i.e. the prebiotic Earth timescale) or so to experiment in organic chemistry. The land-sea interface (such as tidal pools) are a good candidate site since these are areas where high concentrations of organic goodies can be found.

In this context, one focus that researchers have been looking at is self-replicating molecules.

For example, one lab in Cambridge,UK has come up with tC19Z.

tC19Z is the name of a RNA enzyme that acts like a self-replicating molecule. It can copy chunks of RNA almost 50% as long as itself. It can also make copies of other RNA enzymes. This molecule is not "alive" itself, but clearly demonstrates how greater complexity can arise.


They teach us in Physics that the entropy of an isolated system is always increasing or at least constant. Then how can an organism be born under these conditions?

The sun sends energy to the Earth, allowing for a decrease in entropy on Earth at the expense of the sun's entropy.

But when I think about it, all of them assume that there was an organism, however simple, that was capable of self replication & occasionally mutate. How did such an organism come into existence? Can anyone explain this?

That organism you're talking about is just a molecule that copies itself. Exactly how it has come about is not clear to me but it's not hard to imagine the possibility. A vast planet with molecules flying all over being bathed in ultraviolet light and if any molecule anywhere acquires the characteristic of copying itself, it will start growing exponentially and quickly spread all over the world.


This is an extremely interesting and extremely fundamental question, indeed, and thus far, biologists have failed at coming up with a satisfying answer.

We know that all the parts are there, we just don't know how they were arranged, or which ones go where.

The question is, in essence, composed of three sub-questions:

  1. How did the fundamental building blocks of life come about?
  2. How did the first self-replicating molecules come about?
  3. How did cell membranes come about?

The answer generally takes the form of "On primordial Earth, a small selection of the billions of organic compounds generated when UV-light hits a mess of carbon dioxide, nitrogen and water where captured in a tide pool where concentration and foam led to random chance producing self-replicating molecules in proto-cells."

This answer, while almost certainly true, is also incredibly dissatisfying, because all it tells us is what deductive logic has already taught us, almost intuitively.

Incidentally, the fact that all of this happens with a million to one odds isn't a problem: The Earth is big, and the time frame for this happening is along the lines of hundreds of millions of years: Anything that might happen once per year by a million to one shot would likely happen hundreds of times in that timeframe.

In any case, when it comes to evolution, or Darwin's Theory of Evolution, or any other theory of evolution, this is all irrelevant.

Evolution is something that happens in any sufficiently complex (open) system, assuming it has the capacity to change at all.

It is most easily observed in living organisms, because they are at the right scale, and incredibly diverse, but it happens on all scales of the universe.

In fact, the easiest way to explain how life first originated, is just to keep counting backwards when you reach the Last Common Ancestor (of All Life on Earth), and propose models for how this proto-bacterium could be even simpler, until you're left with CO₂, N₂ and H₂O, and other simple molecules.

At that end of the spectrum it is well-understood that e.g. H₂O "evolves" from H₂ and O₂, because H₂O has a quality that makes it more "fit" than either of its components, chemical stability.

Furthermore, H2 "evolves" from free hydrogen by a similar mechanism, and free hydrogen "evolves" from protons and electrons, because it has the property of being electrically neutral, which is also a desirable property.

Of course, at the level of protons and electrons, things get a little muddy, and evolution kind of breaks down as a method for explaining how things come about.

Edit: For reference: Current Models of Abiogenesis on Wikipedia.


While many point to RNA, or a variant of it, as being the first molecule of "life" very few people know where it came from. Some suggest that it came from outer space because it's uncertain how the material for sugar-phosphate backbones could have developed on earth and that the perhaps these materials found their way here via meteorites. There are several hypotheses as to how an early earth environment may have promoted the properties of these molecules, but it's difficult to ascertain what exactly happened.

Somewhere within that abiogenesis wikipedia article is the mention of the role of deep-sea vents. The deep-sea vents and the currents that surround them basically facilitated a PCR reaction. Some of the early emerging DNA, maybe with some RNA and free nucleotides floating around, could have leveraged such an environment for replication and by sheer number (and some chance) entered into symbiotic relationship with other molecules to form the first cellular structures.


If you are interested in this question, I highly recommend you look at the work of Jack Szostak - Nobel Prize winner at Harvard who is currently doing some of the best work in this area. His work is grounded in good experiments that point to how abiogenesis could have happened.


I think that it started like this:

First stage:

Chemicals like Na, Cl, O₂, O₃, CO₂, CO, HCN, and H₂SO₄ react to form small molecules.

Second Stage:

Next those small molecules react to form macromolecules.

Third Stage:

DNA, being the most stable was first to replicate. A membrane eventually enveloped this and formed the nucleus

Fourth Stage:

Via Endosymbiosis it envelops mitochondria in an outer membrane

Fifth Stage:

Cell starts forming membrane and protein for all of its organelles. It is now a eukaryotic cell.

This is the DNA world Hypothesis.

Because DNA can be single, double, triple, or quadruple stranded in organisms(That would be ssDNA, dsDNA, tsDNA, and qsDNA respectively) it can do much more than just code for proteins or rRNA or tRNA.

In the single stranded state it can act like an enzyme forming deoxyribozymes.

In the triple and quadruple stranded states it can act inhibitory without needing another protein or methyl group.


ELI5: How did the first single-celled organism come into existence? Did all life originate from that organism?

The first replicator may not have been a whole cell. It need only have been something capable of replicating itself. EDIT: We don't know how it started. (Yet).

All life on Earth is generally believed to have originated from the first living organism on Earth, yes. There's some debate over the possibility that the first replicators may have developed somewhere besides Earth and been spread here (by meteors or some such). This is mostly only a concern if we want to know whether any hypothetical aliens on other planets are descended from some original replicators, or if life has independently popped up on multiple planets, or what. But life ON EARTH is believed to have all descended from whatever the first cell(s) on Earth were.

Carbon is an atom very common on Earth, and it has the amazing ability to bond with other atoms, forming very complex molecules. This ability of carbon enables all known forms of life, hence why we are called "carbon based life-forms".

In the atmosphere of the early Earth, molecules called monomers were formed, which have the ability to attach to other molecules, and form organic compounds. These monomers collected on the surface of the ocean and were pulled to shore by waves, where they were heavily concentrated in sea foam.

Ever notice the nasty foam on the beach, pushed further and further onto the sand by the waves? The reason it's so nasty is because the waves force a bunch of the crap in the ocean where it gets caught on the sand. In the early Earth, that crap was primarily the monomers from the atmosphere and they all collected in this foam.

With such high concentration, many organic molecules were formed and stuck together with all sorts of stuff near it. Eventually, life arose by sheer chance from this soup of organic molecules.

We do not know. There is no theory to explain it. There are various hypothesis on it but none are considered as well established and they have a lot of holes.

It is strongly believed that all life on earth originated from a common ancestor. For one thing, there are many similarities between cells, DNA, RNA, and proteins of all of the various types of organisms. In particular, the code for turning RNA information into proteins is both very complex and almost identical among all known life, so chances are that it wouldn't have arisen that exact way independently many times - it probably happened once and then evolved into different life forms from there. Scientists believe that bacteria evolved first, then the first simple 1-celled non-bacteria like amoebas and algae, and only much later multicellular animals and plants. Some 1-celled organisms form large colonies of that same life form. The theory of how multicellular life evolved from 1-celled life is that over time different parts of a colony of 1-celled organisms became specialized to perform different functions for the colony, and eventually reproduced that way as performing one function for the whole colony instead of being an independent life form.

How life arose is a much more difficult question, and biologists still aren't sure. The Miller-Urey experiment showed that lightning and minerals that were believed to have been common in the ocean in early earth could have produced basic organic molecules like sugars, amino acids, and proteins. The question is how you get from that to a self-replicating cell. If you consider that it took hundreds of millions of years for life to arise on earth, at some point enough of those molecules got together to form something like RNA, and then that produced a cell that could produce proteins and duplicate its RNA.


How Evolution Works

In order for the principles of mutation and natural selection in the theory of evolution to work, there have to be living things for them to work on. Life must exist before it can to start diversifying. Life had to come from somewhere, and the theory of evolution proposes that it arose spontaneously out of the inert chemicals of planet Earth perhaps 4 billion years ago.

Could life arise spontaneously? If you read How Cells Work, you can see that even a primitive cell like an E. coli bacteria -- one of the simplest life forms in existence today -- is amazingly complex. Following the E. coli model, a cell would have to contain at an absolute minimum:

  • A cell wall of some sort to contain the cell
  • A genetic blueprint for the cell (in the form of DNA)
  • An enzyme capable of copying information out of the genetic blueprint to manufacture new proteins and enzymes
  • An enzyme capable of manufacturing new enzymes, along with all of the building blocks for those enzymes
  • An enzyme that can build cell walls
  • An enzyme able to copy the genetic material in preparation for cell splitting (reproduction)
  • An enzyme or enzymes able to take care of all of the other operations of splitting one cell into two to implement reproduction (For example, something has to get the second copy of the genetic material separated from the first, and then the cell wall has to split and seal over in the two new cells.)
  • Enzymes able to manufacture energy molecules to power all of the previously mentioned enzymes

Obviously, the E. coli cell itself is the product of billions of years of evolution, so it is complex and intricate -- much more complex than the first living cells. Even so, the first living cells had to possess:

  • A cell wall
  • The ability to maintain and expand the cell wall (grow)
  • The ability to process "food" (other molecules floating outside the cell) to create energy
  • The ability to split itself to reproduce

Otherwise, it is not really a cell and it is not really alive. To try to imagine a primordial cell with these capabilities spontaneously creating itself, it is helpful to consider some simplifying assumptions. For example:

  • Perhaps the original energy molecule was very different from the mechanism found in living cells today, and the energy molecules happened to be abundant and free-floating in the environment. Therefore, the original cell would not have had to manufacture them.
  • Perhaps the chemical composition of the Earth was conducive to the spontaneous production of protein chains, so the oceans were filled with unimaginable numbers of random chains and enzymes.
  • Perhaps the first cell walls were naturally forming lipid spheres, and these spheres randomly entrapped different combinations of chemicals.
  • Perhaps the first genetic blueprint was something other than DNA.

These examples do simplify the requirements for the "original cell," but it is still a long way to spontaneous generation of life. Perhaps the first living cells were completely different from what we see today, and no one has yet imagined what they might have been like. Speaking in general terms, life can only have come from one of two possible places:

  • Spontaneous creation - Random chemical processes created the first living cell.
  • Supernatural creation - God or some other supernatural power created the first living cell.

And it doesn't really matter if aliens or meteorites brought the first living cell to earth, because the aliens would have come into existence through either spontaneous creation or supernatural creation at some point -- something had to create the first alien cells.

Most likely, it will be many years before research can completely answer any of the three questions mentioned here. Given that DNA was not discovered until the 1950s, the research on this complicated molecule is still in its infancy, and we have much to learn.


How did the first self replicating organism come into existence? - Biology

Virtually all biologists now agree that bacterial cells cannot form from nonliving chemicals in one step. If life arises from nonliving chemicals, there must be intermediate forms, "precellular life." Of the various theories of precellular life, the leading contender is the RNA world.

RNA has the ability to act as both genes and enzymes. This property could offer a way around the "chicken-and-egg" problem. (Genes require enzymes enzymes require genes.) Furthermore, RNA can be transcribed into DNA, in reverse of the normal process of transcription. These facts are reasons to consider that the RNA world could be the original pathway to cells. James Watson enthusiastically praises Sir Francis Crick for having suggested this possibility (1):

It was prescient of Crick to guess that RNA could act as an enzyme, because that was not known for sure until it was proven in the 1980s by Nobel prize-winning researcher Thomas R. Cech (2) and others. The discovery of RNA enzymes launched a round of new theorizing that is still under way. The term "RNA world" was first used in a 1986 article by Harvard molecular biologist Walter Gilbert (3):

The first stage of evolution proceeds, then, by RNA molecules performing the catalytic activities necessary to assemble themselves from a nucleotide soup. The RNA molecules evolve in self-replicating patterns, using recombination and mutation to explore new niches. . they then develop an entire range of enzymic activities. At the next stage, RNA molecules began to synthesize proteins, first by developing RNA adaptor molecules that can bind activated amino acids and then by arranging them according to an RNA template using other RNA molecules such as the RNA core of the ribosome. This process would make the first proteins, which would simply be better enzymes than their RNA counterparts. . These protein enzymes are . built up of mini-elements of structure.

Finally, DNA appeared on the scene, the ultimate holder of information copied from the genetic RNA molecules by reverse transcription. . RNA is then relegated to the intermediate role it has today—no longer the center of the stage, displaced by DNA and the more effective protein enzymes.

There is a lot to learn about RNA, and research like this is how we learn it. But these and other similar findings, arrived at in highly orchestrated experiments that may start with biologically produced RNA, are very far from proving that the RNA world is the pathway between nonlife and life. In nature, far from the sterilized laboratory, uncontaminated RNA strands of any size would be unlikely to form in the first place. ". The direct synthesis of . nucleotides from prebiotic precursors in reasonable yield and unaccompanied by larger amounts of unrelated molecules could not be achieved by presently known chemical reactions" (5).

At the Salk Institute for Biological Studies, in 1994, Leslie Orgel observes, "Because synthesizing nucleotides and achieving replication of RNA under plausible prebiotic conditions have proved so challenging, chemists are increasingly considering the possibility that RNA was not the first self replicating molecule. " (9).

Apparently NASA has lost enthusiasm for the RNA world as well. In the Final Report issued after the "Astrobiology Workshop" held September 9-11, 1996 at Ames Research Center, California, we read (10),

Other Theories

  • A few scientists still say that DNA could succeed in starting life on its way (11). But even the shortest DNA strand needs proteins to help it replicate. This is the chicken-and-egg problem.
  • There is a "proteins first" school. For example, Manfred Eigen of Germany's Max Planck Institute says, "There is no doubt that proteins, which are more easily formed, were first on the scene" (11.5). Of course, these first proteins must be much shorter than the ones used in life today, because of the sheer unlikelihood of forming useful long ones out of a soup of amino acids.
  • Physicist Freeman Dyson proposes to solve the chicken-and-egg problem with a double origin, one for metabolism (proteins) and one for replication (strands of nucleotides) (12).
  • In Seven Clues to the Origin of Life(13), A. G. Cairns-Smith says that clay crystals could have served as the scaffolding upon which the first short DNA or RNA genome was constructed. A new elaboration of this idea prompted one writer to wonder, "Primordial soup or crêpes?" (14). Even more recently, another tangent on this path leads to zeolite (14.5).
  • Biologists Harold J. Morowitz (15), David Deamer (16), and others (17), advocate a theory that could be paraphrased as "containers first."
  • Jeffrey L. Bada of the Scripps Institution of Oceanography holds the minority view that the early Earth was frozen and believes precellular life started in "cold soup" under the ice (18, 19).
  • Chemists Claudia Huber and Günter Wächtershäuser say the soup where life originated was actually quite hot, probably near undersea volcanic vents, where iron and nickel sulfides might catalyze some of the necessary reactions (19.5-19.7).
  • Cornell Astronomer Thomas Gold wonders if life might have originated in a hot environment even deeper, in Earth's crust (19.8).
  • Stuart Kauffman of the Santa Fe Institute, says, ". whenever a collection of molecules contains enough different kinds of molecules, a metabolism will crystallize from the broth" (20).
  • Another idea is the "PNA world." Because starting the RNA world is so difficult, there probably needs to be a pre-RNA world. PNA, or peptide nucleic acid, might have some of the properties necessary to constitute that world (21). This would be pre-precellular life.
  • Links to several hundred more suggestions appear under What'sNEW, below.

The Time Problem

To go from a bacterium to people is less of a step than to go from a mixture of amino acids to a bacterium. — Lynn Margulis (21.5)

The only premise that all of the precellular theories share is that it would be an extremely long time before the first bacterial cells evolved. If precellular life somehow got going, it could then conceivably begin to crank out, by some precellular process, random strings of nucleotides and amino acids, trying to luck into a gene or a protein with advantages which would lead to bacterial life. There is no evidence in life today of anything that produces huge quantities of new, random strings of nucleotides or amino acids, some of which are advantageous. But if precellular life did that, it would need lots of time to create any useful genes or proteins. How long would it need? After making some helpful assumptions we can get the ratio of actual, useful proteins to all possible random proteins up to something like one in 10^500 (ten to the 500th power). So it would take, barring incredible luck, something like 10^500 trials to probably find one. Imagine that every cubic quarter-inch of ocean in the world contains ten billion precellular ribosomes. Imagine that each ribosome produces proteins at ten trials per minute (about the speed that a working ribosome in a bacterial cell manufactures proteins). Even then, it would take about 10^450 years to probably make one useful protein. But Earth was formed only about 4.6 x 10^9 years ago. The amount of time available for this hypothetical protein creation process was maybe a few hundred million or

10^8 years. And now, to make a cell, we need not just one protein, but a minimum of several hundred.

So even if we allow precellular life, there is a problem getting from there to proteins, genes and cells. The random production of proteins does not succeed as an explanation. Other intermediate, unspecified stages must be imagined. We could call these stages post-precellular life. By whatever means, life's evolution through these stages would have to be time-consuming.

One advocate of the RNA world, Gerald Joyce, allows 400 million years for "The Rise and Fall of the RNA World" (22):

But other researchers see evidence for prokaryotic cells in the first 100 million years, maybe even immediately. ". Actual cells have been found in the earth's oldest unmetamorphosed sediments. " says Gould in Wonderful Life (23). Bada says that cyanobacteria may have emerged only ten million years after the first precellular life (24). In November, 1996, S. J. Mojzsis of the Scripps institution of Oceanography and others reported isotopic evidence that cellular metabolism was under way before 3.8 billion years ago (25). Even before the research by Mojzsis et al., Francis Crick was worried by the time problem. ". The real fossil record suggests that our present form of protein based life was already in existence 3.6 billion years ago. This leaves an astonishingly short time to get life started" (26). Another researcher, Yale biochemist Peter B. Moore, says this about the time problem (27):

Of one thing we can be certain: The RNA world—if it ever existed—was short-lived. The earth came into existence about 4.5 x 10^9 years ago, and fossil evidence suggests that cellular organisms resembling modern bacteria existed by 3.6 x 10^9 years before the present. There are even hints that those early organisms engaged in photosynthesis, which is likely to have been a protein-dependent process then, as now. Thus it appears likely that organisms with sophisticated, protein based metabolisms existed only 0.9 x 10^9 years after the planet's birth.

The "window of opportunity" for the RNA world was much shorter than 0.9 x 10^9 years. The earth's surface was uninhabitable at the beginning due to heat generated by meteoric bombardment and its geological differentiation. . Thus, the interval in which the biosphere could have been dominated by RNA-based life forms may be less than 100 million years. Incidentally, when one starts thinking along these lines, one must consider the unthinkable, i.e., that the length of time that RNA-based proteins actually bestrode the earth might be zero.

Summary

  • There is no remnant or trace evidence of precellular life anywhere today. That it ever existed is entirely conjectural.
  • Although its emergence from nonliving matter is hard to conceive, precellular life must have appeared almost immediately.
  • There was almost no time for precellular life to evolve into the simplest bacterial cells.
  • Precellular life has never been created in a lab.
  • In spite of the RNA world, there is no consensus on the model for precellular life.

We said that research in the RNA world is a medium-sized industry. This research has demonstrated how exceedingly difficult it would be for living cells to originate by chance from nonliving matter in the time available on Earth. That demonstration is a valuable contribution to science. Additional research will be valuable as well. But to keep insisting that life can spontaneously emerge from nonliving chemicals in the face of the newly comprehended difficulties is puzzling. It is reminiscent of the persistent efforts of medieval alchemists to turn lead into gold.

There is another scientific explanation for the origin of life on Earth. It is that whole cells arrived here from space. (Life "in the first place" is a separate issue, dealt with elsewhere on this website.)

What'sNEW

The fossil record indicates that there were handheld calculators with at least 240 kilobytes of stored programs in existence almost as soon as the earth cooled. Possibly, handheld calculators originated when special conditions allowed the formation of silicon chips and circuit boards (primitive genes). Heat, perhaps generated by radioactivity, volcanoes or meteor impacts, melted some sand to form a silicon flake. Random splashing of molten metal caused metal filaments to form a circuit board on the flake. Oily film on ponds dried into the hard plastic material needed for the shell.

Lightning provided the first source of electrical power. Prototypes in seawater, at just the right distance from the strike, received sufficient voltage without being destroyed. Batteries (allowing independent metabolism) came later. The first batteries were iron acid batteries, formed in mud pockets. Lithium batteries were a very late development.


How did the first self replicating organism come into existence? - Biology

Where does Life come from?

The origin of life or prebiotic evolution means the spontaneous generation of life in a 'primordial soup' containing small organic molecules in salt water. Such a process is generally believed not to be possible (or successful) in today's ecosystems, unless undertaken in controlled laboratory settings. The latter awaits experimental proof. In order to understand the spontaneous formation of life an appropriate definition of life must be at hand. Derived from an analysis of today's organisms life is usually defined at the cellular level. In this definition, the smallest or simplest forms of life are single cell organisms which include bacteria, archaea (halophiles and thermophiles live in extreme environments), and protozoans (eukaryotic single celled microorganisms, e.g. baker's yeast, paramecium, or amoebae). All modern life forms share fundamental molecular mechanisms, most notably protein biosynthesis and the use of DNA and RNA for reproduction and energy metabolism. Based on these observations, theories on the origin of life attempt to find a mechanism explaining the formation of a primordial single cell organism from which all modern life originates. The primordial cell is thought to form itself through beneficial packaging of self-replicating units in lipid particles (liposomes or vesicles resembling modern cell membranes). The most pressing question is how closely modern organisms resemble a primordial cell. Evidence of prebiotic evolution is obtained through simulating and replicating such an event that happened about 3.5 billion years ago. Although biochemical evidence first obtained in the 1950s showed the spontaneous generation of amino acids in a replica of the 'primordial soup', most biologist now believe that amino acids which are the building blocks of proteins and peptides, today's essential tools in all life forms, were not important at this earliest stage and that proteins and enzymes were indeed preceded by RNA type molecules which still plays an essential role in modern metabolism including energy metabolism, enzymatic catalysis (e.g. protein biosynthesis), and processing and storage of genetic information. DNA, this modern molecular marvel and blueprint of life, may indeed have come into existence after the evolution of proteins as enzymes.

Over the last few years analysis of rocks found in Antarctic ice sheets and originating from Mars contain microstructures consistent with leftovers of Martian organisms because these structures so closely resemble structures or leftovers from bacteria on Earth. The interpretation of whether these deposits are really proof of (ancient) life on Mars are controversial but of enormous interest to biologists. Single celled life on Mars, even if extinct today, would corroborate origin of life theories. Proven or not, the possibility of a future prove is enough to stimulate research including theory building on speculative grounds. It is these theories vaguely supported by experimental evidence (fossil evidence in this case) that will spurn imagination and the design of experimental protocols to actively explore the Martian soil and atmosphere. A note of caution even if future analysis would prove that life existed on Mars, it would leave open the possibilities that life has been imported from Earth or life on Earth originated from Mars (or some place else). What ever the outcome, the current quest of proving the ancient existence of life on Mars at least gives an excellent example of how scientists work and draw conclusions from observations when events cannot be recreated in the laboratory under controlled conditions as is the case in studying the evolution of life.


Contents

One of the challenges in studying abiogenesis is that the system of reproduction and metabolism utilized by all extant life involves three distinct types of interdependent macromolecules (DNA, RNA, and protein). This suggests that life could not have arisen in its current form, which has led researchers to hypothesize mechanisms whereby the current system might have arisen from a simpler precursor system. The concept of RNA as a primordial molecule [2] can be found in papers by Francis Crick [12] and Leslie Orgel, [13] as well as in Carl Woese's 1967 book The Genetic Code. [14] In 1962, the molecular biologist Alexander Rich posited much the same idea in an article he contributed to a volume issued in honor of Nobel-laureate physiologist Albert Szent-Györgyi. [15] Hans Kuhn in 1972 laid out a possible process by which the modern genetic system might have arisen from a nucleotide-based precursor, and this led Harold White in 1976 to observe that many of the cofactors essential for enzymatic function are either nucleotides or could have been derived from nucleotides. He proposed a scenario whereby the critical electrochemistry of enzymatic reactions would have necessitated retention of the specific nucleotide moieties of the original RNA-based enzymes carrying out the reactions, while the remaining structural elements of the enzymes were gradually replaced by protein, until all that remained of the original RNAs were these nucleotide cofactors, "fossils of nucleic acid enzymes". [16] The phrase "RNA World" was first used by Nobel laureate Walter Gilbert in 1986, in a commentary on how recent observations of the catalytic properties of various forms of RNA fit with this hypothesis. [17]

The properties of RNA make the idea of the RNA world hypothesis conceptually plausible, though its general acceptance as an explanation for the origin of life requires further evidence. [15] RNA is known to form efficient catalysts and its similarity to DNA makes clear its ability to store information. Opinions differ, however, as to whether RNA constituted the first autonomous self-replicating system or was a derivative of a still-earlier system. [2] One version of the hypothesis is that a different type of nucleic acid, termed pre-RNA, was the first one to emerge as a self-reproducing molecule, to be replaced by RNA only later. On the other hand, the discovery in 2009 that activated pyrimidine ribonucleotides can be synthesized under plausible prebiotic conditions [18] suggests that it is premature to dismiss the RNA-first scenarios. [2] Suggestions for 'simple' pre-RNA nucleic acids have included peptide nucleic acid (PNA), threose nucleic acid (TNA) or glycol nucleic acid (GNA). [19] [20] Despite their structural simplicity and possession of properties comparable with RNA, the chemically plausible generation of "simpler" nucleic acids under prebiotic conditions has yet to be demonstrated. [21]

RNA as an enzyme Edit

RNA enzymes, or ribozymes, are found in today's DNA-based life and could be examples of living fossils. Ribozymes play vital roles, such as that of the ribosome. The large subunit of the ribosome includes an rRNA responsible for the peptide bond-forming peptidyl transferase activity of protein synthesis. Many other ribozyme activities exist for example, the hammerhead ribozyme performs self-cleavage [22] and an RNA polymerase ribozyme can synthesize a short RNA strand from a primed RNA template. [23]

Among the enzymatic properties important for the beginning of life are:

Self-replication The ability to self-replicate, or synthesize other RNA molecules relatively short RNA molecules that can synthesize others have been artificially produced in the lab. The shortest was 165 bases long, though it has been estimated that only part of the molecule was crucial for this function. One version, 189 bases long, had an error rate of just 1.1% per nucleotide when synthesizing an 11 nucleotide long RNA strand from primed template strands. [24] This 189 base pair ribozyme could polymerize a template of at most 14 nucleotides in length, which is too short for self replication, but is a potential lead for further investigation. The longest primer extension performed by a ribozyme polymerase was 20 bases. [25] In 2016, researchers reported the use of in vitro evolution to improve dramatically the activity and generality of an RNA polymerase ribozyme by selecting variants that can synthesize functional RNA molecules from an RNA template. Each RNA polymerase ribozyme was engineered to remain linked to its new, synthesized RNA strand this allowed the team to isolate successful polymerases. The isolated RNA polymerases were again used for another round of evolution. After several rounds of evolution, they obtained one RNA polymerase ribozyme called 24-3 that was able to copy almost any other RNA, from small catalysts to long RNA-based enzymes. Particular RNAs were amplified up to 10,000 times, a first RNA version of the polymerase chain reaction (PCR). [26] Catalysis The ability to catalyze simple chemical reactions—which would enhance creation of molecules that are building blocks of RNA molecules (i.e., a strand of RNA that would make creating more strands of RNA easier). Relatively short RNA molecules with such abilities have been artificially formed in the lab. [27] [28] A recent study showed that almost any nucleic acid can evolve into a catalytic sequence under appropriate selection. For instance, an arbitrarily chosen 50-nucleotide DNA fragment encoding for the Bos taurus (cattle) albumin mRNA was subjected to test-tube evolution to derive a catalytic DNA (Deoxyribozyme, also called DNAzyme) with RNA-cleavage activity. After only a few weeks, a DNAzyme with significant catalytic activity had evolved. [29] In general, DNA is much more chemically inert than RNA and hence much more resistant to obtaining catalytic properties. If in vitro evolution works for DNA it will happen much more easily with RNA. Amino acid-RNA ligation The ability to conjugate an amino acid to the 3'-end of an RNA in order to use its chemical groups or provide a long-branched aliphatic side-chain. [30] Peptide bond formation The ability to catalyse the formation of peptide bonds between amino acids to produce short peptides or longer proteins. This is done in modern cells by ribosomes, a complex of several RNA molecules known as rRNA together with many proteins. The rRNA molecules are thought responsible for its enzymatic activity, as no amino-acid residues lie within 18Å of the enzyme's active site, [15] and, when the majority of the amino-acid residues in the ribosome were stringently removed, the resulting ribosome retained its full peptidyl transferase activity, fully able to catalyze the formation of peptide bonds between amino acids. [31] A much shorter RNA molecule has been synthesized in the laboratory with the ability to form peptide bonds, and it has been suggested that rRNA has evolved from a similar molecule. [32] It has also been suggested that amino acids may have initially been involved with RNA molecules as cofactors enhancing or diversifying their enzymatic capabilities, before evolving into more complex peptides. Similarly, tRNA is suggested to have evolved from RNA molecules that began to catalyze amino acid transfer. [33]

RNA in information storage Edit

RNA is a very similar molecule to DNA, with only two major chemical differences (the backbone of RNA uses ribose instead of deoxyribose and its nucleobases include uracil instead of thymine). The overall structure of RNA and DNA are immensely similar—one strand of DNA and one of RNA can bind to form a double helical structure. This makes the storage of information in RNA possible in a very similar way to the storage of information in DNA. However, RNA is less stable, being more prone to hydrolysis due to the presence of a hydroxyl group at the ribose 2' position.

Comparison of DNA and RNA structure Edit

The major difference between RNA and DNA is the presence of a hydroxyl group at the 2'-position of the ribose sugar in RNA (illustration, right). [15] This group makes the molecule less stable because, when not constrained in a double helix, the 2' hydroxyl can chemically attack the adjacent phosphodiester bond to cleave the phosphodiester backbone. The hydroxyl group also forces the ribose into the C3'-endo sugar conformation unlike the C2'-endo conformation of the deoxyribose sugar in DNA. This forces an RNA double helix to change from a B-DNA structure to one more closely resembling A-DNA.

RNA also uses a different set of bases than DNA—adenine, guanine, cytosine and uracil, instead of adenine, guanine, cytosine and thymine. Chemically, uracil is similar to thymine, differing only by a methyl group, and its production requires less energy. [34] In terms of base pairing, this has no effect. Adenine readily binds uracil or thymine. Uracil is, however, one product of damage to cytosine that makes RNA particularly susceptible to mutations that can replace a GC base pair with a GU (wobble) or AU base pair.

RNA is thought to have preceded DNA, because of their ordering in the biosynthetic pathways. The deoxyribonucleotides used to make DNA are made from ribonucleotides, the building blocks of RNA, by removing the 2'-hydroxyl group. As a consequence a cell must have the ability to make RNA before it can make DNA.

Limitations of information storage in RNA Edit

The chemical properties of RNA make large RNA molecules inherently fragile, and they can easily be broken down into their constituent nucleotides through hydrolysis. [35] [36] These limitations do not make use of RNA as an information storage system impossible, simply energy intensive (to repair or replace damaged RNA molecules) and prone to mutation. While this makes it unsuitable for current 'DNA optimised' life, it may have been acceptable for more primitive life.

RNA as a regulator Edit

Riboswitches have been found to act as regulators of gene expression, particularly in bacteria, but also in plants and archaea. Riboswitches alter their secondary structure in response to the binding of a metabolite. This change in structure can result in the formation or disruption of a terminator, truncating or permitting transcription respectively. [37] Alternatively, riboswitches may bind or occlude the Shine–Dalgarno sequence, affecting translation. [38] It has been suggested that these originated in an RNA-based world. [39] In addition, RNA thermometers regulate gene expression in response to temperature changes. [40]

The RNA world hypothesis is supported by RNA's ability both to store, transmit, and duplicate genetic information, as DNA does, and to perform enzymatic reactions, like protein-based enzymes. Because it can carry out the types of tasks now performed by proteins and DNA, RNA is believed to have once been capable of supporting independent life on its own. [15] Some viruses use RNA as their genetic material, rather than DNA. [41] Further, while nucleotides were not found in experiments based on Miller-Urey experiment, their formation in prebiotically plausible conditions was reported in 2009 [18] a purine base, adenine, is merely a pentamer of hydrogen cyanide. Experiments with basic ribozymes, like Bacteriophage Qβ RNA, have shown that simple self-replicating RNA structures can withstand even strong selective pressures (e.g., opposite-chirality chain terminators). [42]

Since there were no known chemical pathways for the abiogenic synthesis of nucleotides from pyrimidine nucleobases cytosine and uracil under prebiotic conditions, it is thought by some that nucleic acids did not contain these nucleobases seen in life's nucleic acids. [43] The nucleoside cytosine has a half-life in isolation of 19 days at 100 °C (212 °F) and 17,000 years in freezing water, which some argue is too short on the geologic time scale for accumulation. [44] Others have questioned whether ribose and other backbone sugars could be stable enough to be found in the original genetic material, [45] and have raised the issue that all ribose molecules would have had to be the same enantiomer, as any nucleotide of the wrong chirality acts as a chain terminator. [46]

Pyrimidine ribonucleosides and their respective nucleotides have been prebiotically synthesised by a sequence of reactions that by-pass free sugars and assemble in a stepwise fashion by including nitrogenous and oxygenous chemistries. In a series of publications, John Sutherland and his team at the School of Chemistry, University of Manchester, have demonstrated high yielding routes to cytidine and uridine ribonucleotides built from small 2- and 3-carbon fragments such as glycolaldehyde, glyceraldehyde or glyceraldehyde-3-phosphate, cyanamide, and cyanoacetylene. One of the steps in this sequence allows the isolation of enantiopure ribose aminooxazoline if the enantiomeric excess of glyceraldehyde is 60% or greater, of possible interest toward biological homochirality. [47] This can be viewed as a prebiotic purification step, where the said compound spontaneously crystallised out from a mixture of the other pentose aminooxazolines. Aminooxazolines can react with cyanoacetylene in a mild and highly efficient manner, controlled by inorganic phosphate, to give the cytidine ribonucleotides. Photoanomerization with UV light allows for inversion about the 1' anomeric centre to give the correct beta stereochemistry one problem with this chemistry is the selective phosphorylation of alpha-cytidine at the 2' position. [48] However, in 2009, they showed that the same simple building blocks allow access, via phosphate controlled nucleobase elaboration, to 2',3'-cyclic pyrimidine nucleotides directly, which are known to be able to polymerise into RNA. [18] Organic chemist Donna Blackmond described this finding as "strong evidence" in favour of the RNA world. [49] However, John Sutherland said that while his team's work suggests that nucleic acids played an early and central role in the origin of life, it did not necessarily support the RNA world hypothesis in the strict sense, which he described as a "restrictive, hypothetical arrangement". [50]

The Sutherland group's 2009 paper also highlighted the possibility for the photo-sanitization of the pyrimidine-2',3'-cyclic phosphates. [18] A potential weakness of these routes is the generation of enantioenriched glyceraldehyde, or its 3-phosphate derivative (glyceraldehyde prefers to exist as its keto tautomer dihydroxyacetone). [ citation needed ]

On August 8, 2011, a report, based on NASA studies with meteorites found on Earth, was published suggesting building blocks of RNA (adenine, guanine, and related organic molecules) may have been formed extraterrestrially in outer space. [51] [52] [53] In 2017, a numerical model suggests that the RNA world may have emerged in warm ponds on the early Earth, and that meteorites were a plausible and probable source of the RNA building blocks (ribose and nucleic acids) to these environments. [54] On August 29, 2012, astronomers at Copenhagen University reported the detection of a specific sugar molecule, glycolaldehyde, in a distant star system. The molecule was found around the protostellar binary IRAS 16293-2422, which is located 400 light years from Earth. [55] [56] Because glycolaldehyde is needed to form RNA, this finding suggests that complex organic molecules may form in stellar systems prior to the formation of planets, eventually arriving on young planets early in their formation. [57]

Nucleotides are the fundamental molecules that combine in series to form RNA. They consist of a nitrogenous base attached to a sugar-phosphate backbone. RNA is made of long stretches of specific nucleotides arranged so that their sequence of bases carries information. The RNA world hypothesis holds that in the primordial soup (or sandwich), there existed free-floating nucleotides. These nucleotides regularly formed bonds with one another, which often broke because the change in energy was so low. However, certain sequences of base pairs have catalytic properties that lower the energy of their chain being created, enabling them to stay together for longer periods of time. As each chain grew longer, it attracted more matching nucleotides faster, causing chains to now form faster than they were breaking down.

These chains have been proposed by some as the first, primitive forms of life. In an RNA world, different sets of RNA strands would have had different replication outputs, which would have increased or decreased their frequency in the population, i.e. natural selection. As the fittest sets of RNA molecules expanded their numbers, novel catalytic properties added by mutation, which benefitted their persistence and expansion, could accumulate in the population. Such an autocatalytic set of ribozymes, capable of self replication in about an hour, has been identified. It was produced by molecular competition (in vitro evolution) of candidate enzyme mixtures. [58]

Competition between RNA may have favored the emergence of cooperation between different RNA chains, opening the way for the formation of the first protocell. Eventually, RNA chains developed with catalytic properties that help amino acids bind together (a process called peptide-bonding). These amino acids could then assist with RNA synthesis, giving those RNA chains that could serve as ribozymes the selective advantage. The ability to catalyze one step in protein synthesis, aminoacylation of RNA, has been demonstrated in a short (five-nucleotide) segment of RNA. [59]

In March 2015, NASA scientists reported that, for the first time, complex DNA and RNA organic compounds of life, including uracil, cytosine, and thymine, have been formed in the laboratory under conditions found only in outer space, using starting chemicals, like pyrimidine, found in meteorites. Pyrimidine, like polycyclic aromatic hydrocarbons (PAHs), may have been formed in red giant stars or in interstellar dust and gas clouds, according to the scientists. [60]

In 2018, researchers at Georgia Institute of Technology identified three molecular candidates for the bases that might have formed an earliest version of proto-RNA: barbituric acid, melamine, and 2,4,6-triaminopyrimidine (TAP). These three molecules are simpler versions of the four bases in current RNA, which could have been present in larger amounts and could still be forward-compatible with them, but may have been discarded by evolution in exchange for more optimal base pairs. [61] Specifically, TAP can form nucleotides with a large range of sugars. [62] Both TAP and melamine base pair with barbituric acid. All three spontaneously form nucleotides with ribose. [63]

One of the challenges posed by the RNA world hypothesis is to discover the pathway by which an RNA-based system transitioned to one based on DNA. Geoffrey Diemer and Ken Stedman, at Portland State University in Oregon, may have found a solution. While conducting a survey of viruses in a hot acidic lake in Lassen Volcanic National Park, California, they uncovered evidence that a simple DNA virus had acquired a gene from a completely unrelated RNA-based virus. Virologist Luis Villareal of the University of California Irvine also suggests that viruses capable of converting an RNA-based gene into DNA and then incorporating it into a more complex DNA-based genome might have been common in the Virus world during the RNA to DNA transition some 4 billion years ago. [64] [65] This finding bolsters the argument for the transfer of information from the RNA world to the emerging DNA world before the emergence of the last universal common ancestor. From the research, the diversity of this virus world is still with us.

Additional evidence supporting the concept of an RNA world has resulted from research on viroids, the first representatives of a novel domain of "subviral pathogens". [66] [67] Viroids are mostly plant pathogens, which consist of short stretches (a few hundred nucleobases) of highly complementary, circular, single-stranded, and non-coding RNA without a protein coat. Compared with other infectious plant pathogens, viroids are extremely small, ranging from 246 to 467 nucleobases. In comparison, the genome of the smallest known viruses capable of causing an infection are about 2,000 nucleobases long. [68]

In 1989, Diener proposed that, based on their characteristic properties, viroids are more plausible "living relics" of the RNA world than are introns or other RNAs then so considered. [69] If so, viroids have attained potential significance beyond plant pathology to evolutionary biology, by representing the most plausible macromolecules known capable of explaining crucial intermediate steps in the evolution of life from inanimate matter (see: abiogenesis).

Apparently, Diener's hypothesis lay dormant until 2014, when Flores et al. published a review paper, in which Diener's evidence supporting his hypothesis was summarized. [70] In the same year, a New York Times science writer published a popularized version of Diener's proposal, in which, however, he mistakenly credited Flores et al. with the hypothesis' original conception. [71]

Pertinent viroid properties listed in 1989 are:

  1. small size, imposed by error-prone replication
  2. high guanine and cytosine content, which increases stability and replication fidelity
  3. circular structure, which assures complete replication without genomic tags
  4. structural periodicity, which permits modular assembly into enlarged genomes
  5. lack of protein-coding ability, consistent with a ribosome-free habitat and
  6. in some cases, replication mediated by ribozymes—the fingerprint of the RNA world. [70]

The existence, in extant cells, of RNAs with molecular properties predicted for RNAs of the RNA World constitutes an additional argument supporting the RNA World hypothesis.

Eigen et al. [72] and Woese [73] proposed that the genomes of early protocells were composed of single-stranded RNA, and that individual genes corresponded to separate RNA segments, rather than being linked end-to-end as in present-day DNA genomes. A protocell that was haploid (one copy of each RNA gene) would be vulnerable to damage, since a single lesion in any RNA segment would be potentially lethal to the protocell (e.g. by blocking replication or inhibiting the function of an essential gene).

Vulnerability to damage could be reduced by maintaining two or more copies of each RNA segment in each protocell, i.e. by maintaining diploidy or polyploidy. Genome redundancy would allow a damaged RNA segment to be replaced by an additional replication of its homolog. However, for such a simple organism, the proportion of available resources tied up in the genetic material would be a large fraction of the total resource budget. Under limited resource conditions, the protocell reproductive rate would likely be inversely related to ploidy number. The protocell's fitness would be reduced by the costs of redundancy. Consequently, coping with damaged RNA genes while minimizing the costs of redundancy would likely have been a fundamental problem for early protocells.

A cost-benefit analysis was carried out in which the costs of maintaining redundancy were balanced against the costs of genome damage. [74] This analysis led to the conclusion that, under a wide range of circumstances, the selected strategy would be for each protocell to be haploid, but to periodically fuse with another haploid protocell to form a transient diploid. The retention of the haploid state maximizes the growth rate. The periodic fusions permit mutual reactivation of otherwise lethally damaged protocells. If at least one damage-free copy of each RNA gene is present in the transient diploid, viable progeny can be formed. For two, rather than one, viable daughter cells to be produced would require an extra replication of the intact RNA gene homologous to any RNA gene that had been damaged prior to the division of the fused protocell. The cycle of haploid reproduction, with occasional fusion to a transient diploid state, followed by splitting to the haploid state, can be considered to be the sexual cycle in its most primitive form. [74] [75] In the absence of this sexual cycle, haploid protocells with damage in an essential RNA gene would simply die.

This model for the early sexual cycle is hypothetical, but it is very similar to the known sexual behavior of the segmented RNA viruses, which are among the simplest organisms known. Influenza virus, whose genome consists of 8 physically separated single-stranded RNA segments, [76] is an example of this type of virus. In segmented RNA viruses, "mating" can occur when a host cell is infected by at least two virus particles. If these viruses each contain an RNA segment with a lethal damage, multiple infection can lead to reactivation providing that at least one undamaged copy of each virus gene is present in the infected cell. This phenomenon is known as "multiplicity reactivation". Multiplicity reactivation has been reported to occur in influenza virus infections after induction of RNA damage by UV-irradiation, [77] and ionizing radiation. [78]

Patrick Forterre has been working on a novel hypothesis, called "three viruses, three domains": [79] that viruses were instrumental in the transition from RNA to DNA and the evolution of Bacteria, Archaea, and Eukaryota. He believes the last universal common ancestor [79] was RNA-based and evolved RNA viruses. Some of the viruses evolved into DNA viruses to protect their genes from attack. Through the process of viral infection into hosts the three domains of life evolved. [79] [80]

Another interesting proposal is the idea that RNA synthesis might have been driven by temperature gradients, in the process of thermosynthesis. [81] Single nucleotides have been shown to catalyze organic reactions. [82]

Steven Benner has argued that chemical conditions on the planet Mars, such as the presence of boron, molybdenum, and oxygen, may have been better for initially producing RNA molecules than those on Earth. If so, life-suitable molecules, originating on Mars, may have later migrated to Earth via mechanisms of panspermia or similar process. [83] [84]

The hypothesized existence of an RNA world does not exclude a "Pre-RNA world", where a metabolic system based on a different nucleic acid is proposed to pre-date RNA. A candidate nucleic acid is peptide nucleic acid (PNA), which uses simple peptide bonds to link nucleobases. [85] PNA is more stable than RNA, but its ability to be generated under prebiological conditions has yet to be demonstrated experimentally.

Threose nucleic acid (TNA) has also been proposed as a starting point, as has glycol nucleic acid (GNA), and like PNA, also lack experimental evidence for their respective abiogenesis.

An alternative—or complementary—theory of RNA origin is proposed in the PAH world hypothesis, whereby polycyclic aromatic hydrocarbons (PAHs) mediate the synthesis of RNA molecules. [86] PAHs are the most common and abundant of the known polyatomic molecules in the visible Universe, and are a likely constituent of the primordial sea. [87] PAHs and fullerenes (also implicated in the origin of life) [88] have been detected in nebulae. [89]

The iron-sulfur world theory proposes that simple metabolic processes developed before genetic materials did, and these energy-producing cycles catalyzed the production of genes.

Some of the difficulties of producing the precursors on earth are bypassed by another alternative or complementary theory for their origin, panspermia. It discusses the possibility that the earliest life on this planet was carried here from somewhere else in the galaxy, possibly on meteorites similar to the Murchison meteorite. [90] Sugar molecules, including ribose, have been found in meteorites. [91] [92] Panspermia does not invalidate the concept of an RNA world, but posits that this world or its precursors originated not on Earth but rather another, probably older, planet.

There are hypotheses that are in direct conflict to the RNA world hypothesis [ citation needed ] . The relative chemical complexity of the nucleotide and the unlikelihood of it spontaneously arising, along with the limited number of combinations possible among four base forms, as well as the need for RNA polymers of some length before seeing enzymatic activity, have led some to reject the RNA world hypothesis in favor of a metabolism-first hypothesis, where the chemistry underlying cellular function arose first, along with the ability to replicate and facilitate this metabolism.

RNA-peptide coevolution Edit

Another proposal is that the dual-molecule system we see today, where a nucleotide-based molecule is needed to synthesize protein, and a peptide-based (protein) molecule is needed to make nucleic acid polymers, represents the original form of life. [93] This theory is called RNA-peptide coevolution, [94] or the Peptide-RNA world, and offers a possible explanation for the rapid evolution of high-quality replication in RNA (since proteins are catalysts), with the disadvantage of having to postulate the coincident formation of two complex molecules, an enzyme (from peptides) and a RNA (from nucleotides). In this Peptide-RNA World scenario, RNA would have contained the instructions for life, while peptides (simple protein enzymes) would have accelerated key chemical reactions to carry out those instructions. [95] The study leaves open the question of exactly how those primitive systems managed to replicate themselves — something neither the RNA World hypothesis nor the Peptide-RNA World theory can yet explain, unless polymerases (enzymes that rapidly assemble the RNA molecule) played a role. [95]

A research project completed in March 2015 by the Sutherland group found that a network of reactions beginning with hydrogen cyanide and hydrogen sulfide, in streams of water irradiated by UV light, could produce the chemical components of proteins and lipids, alongside those of RNA. [96] [97] The researchers used the term "cyanosulfidic" to describe this network of reactions. [96] In November 2017, a team at the Scripps Research Institute identified reactions involving the compound diamidophosphate which could have linked the chemical components into short peptide and lipid chains as well as short RNA-like chains of nucleotides. [98] [99]

The RNA world hypothesis, if true, has important implications for the definition of life. For most of the time that followed Franklin, Watson and Crick's elucidation of DNA structure in 1953, life was largely defined in terms of DNA and proteins: DNA and proteins seemed the dominant macromolecules in the living cell, with RNA only aiding in creating proteins from the DNA blueprint.

The RNA world hypothesis places RNA at center-stage when life originated. The RNA world hypothesis is supported by the observations that ribosomes are ribozymes: [100] [101] the catalytic site is composed of RNA, and proteins hold no major structural role and are of peripheral functional importance. This was confirmed with the deciphering of the 3-dimensional structure of the ribosome in 2001. Specifically, peptide bond formation, the reaction that binds amino acids together into proteins, is now known to be catalyzed by an adenine residue in the rRNA.

RNAs are known to play roles in other cellular catalytic processes, specifically in the targeting of enzymes to specific RNA sequences. In eukaryotes, the processing of pre-mRNA and RNA editing take place at sites determined by the base pairing between the target RNA and RNA constituents of small nuclear ribonucleoproteins (snRNPs). Such enzyme targeting is also responsible for gene down regulation through RNA interference (RNAi), where an enzyme-associated guide RNA targets specific mRNA for selective destruction. Likewise, in eukaryotes the maintenance of telomeres involves copying of an RNA template that is a constituent part of the telomerase ribonucleoprotein enzyme. Another cellular organelle, the vault, includes a ribonucleoprotein component, although the function of this organelle remains to be elucidated.


ELI5: Why did the first organisms replicate?

AFAIK back in the good ol' days when the Earth was one young, hot, primordial soup-a funny thing happened. The stars (stars, complex organic molecules, big diff) aligned and lo and behold! An organism is born! According to my AP Bio textbook the conditions necessary to make this happen was most likely at some hydrothermal vent somewhere.

My question is this: Why (and bonus points for how) did those primitive, first, unicellular organisms replicate? There was no RNA or DNA and even if there was, why would that CAUSE replication?

EDIT: As a couple of users have pointed out, the RNA World hypothesis suggests that the first "organisms" were RNA, which can self replicate.

The very first organisms were basically blobs with very specific materials inside them. When the blobs grew in size they eventually became so big they split in two, sharing whatever innards the original blob had. Presto, extremely primitive reproduction.

This is a good start for an answer.

Iɽ add that being better at reproduction provided an evolutionary benefit - those who had mechanisms which ensured the next generation had sufficient resources to thrive were more likely to pass those mechanisms on.

But what's to say that theyɽ split evenly i.e. both blobs are identical? Why didn't that result in exponential growth of an unfathomable number of unique primitive cells dividing this way?

I don't think an organism by our current definition emerged, but something else. Check out: https://en.wikipedia.org/wiki/RNA_world

Of course it's natural to wonder how RNA came to exist, and that may take us a very long time to discover. I wonder whether mutation was the precursor to replication.

Ah, I remember reading about RNA world hypothesis now. But RNA on it's own cant replicate. Are there any leading theories on how the first RNA molecules pulled that off?

I remember reading that the first few microscopic blobs also took in these little clay crystals. When more crystals grew, they used the previous crystal as a template, producing an exact copy. This ended up being used as primitive genes of sorts before RNA came into existence.

That's interesting, I never heard that theory before. Do you know why they used the previous crystals to replicate? Also Iɽ appreciate any resources on the topic you throw my way.

There was no RNA or DNA and even if there was, why would that CAUSE replication?

That's not true, according to the most widely accepted explanation for this, known as the "RNA world hypothesis." The idea is that the first replicating "organisms" were RNA molecules. Based on the conditions of an early Earth, the building blocks of RNA could form naturally.

One of the cool things about RNA is that it actually can replicate itself to a certain degree. Different bases (pieces of RNA or DNA) match up with particular other bases in a pattern. Furthermore, RNA is just a chain of nucleotides (small, repeating units), so it can add on more bases to become longer or break apart to form shorter chains.

And on top of all of this, RNA has another important property: It can act like an enzyme and catalyze reactions. In other words, RNA can perform chemical reactions, allowing it to perform more complex reactions than merely lengthening and shortening chains. In fact, even in modern cells, RNA (in the ribosomes) is used to make proteins, an incredibly important task for the complex things a cell can do.

To summarize, although it doesn't really count as an organism, the first biological thing reproducing was likely RNA. The conditions on the Earth were conducive to the production of the building blocks of RNA, and RNA has lots of properties that give it the ability to reproduce itself.


2. AN “RNA-FIRST” VIEW OF THE ORIGIN OF LIFE

2.1. Abiotic Synthesis of Polynucleotides

This section considers the synthesis of oligonucleotides from ß- d -nucleoside 5′-phosphates, leaving aside for now the question of how the nucleotides became available on the primitive Earth. Two fundamentally different chemical reactions are involved. First, the nucleotide must be converted to an activated derivative, for example, a nucleoside 5′-polyphosphate. Next the 3′-hydroxyl group of a nucleotide or oligonucleotide molecule must be made to react with the activated phosphate group of a monomer. Synthesis of oligonucleotides from nucleoside 3′-phosphates will not be discussed because activated nucleoside 2′- or 3′-phosphates in general react readily to form 2′,3′-cyclic phosphates. These cyclic phosphates are unlikely to oligomerize efficiently because the equilibrium constant for dimer formation is only of the order of 1.0 L/mol (Erman and Hammes 1966 Mohr and Thach 1969). In the presence of a complementary template somewhat larger oligomers might be formed because the free energy of hybridization would help to drive forward the chain extension reaction.

In enzymatic RNA and DNA synthesis, the nucleoside 5′-triphosphates (NTPs) are the substrates of polymerization. Polynucleotide phosphorylase, although it is a degradative enzyme in nature, can be used to synthesize oligonucleotides from nucleoside 5′-diphosphates. Nucleoside 5′-polyphosphates are, therefore, obvious candidates for the activated forms of nucleotides. Although nucleoside 5′-triphosphates are not formed readily, the synthesis of nucleoside 5′-tetraphosphates from nucleotides and inorganic trimetaphosphate provides a reasonably plausible prebiotic route to activated nucleotides (Lohrmann 1975). Other more or less plausible prebiotic syntheses of nucleoside 5′-polyphosphates from nucleotides have also been reported (Handschuh et al. 1973 Osterberg et al. 1973 Reimann and Zubay 1999). Less clear, however, is how the first phosphate would have been mobilized to convert the nucleosides to 5′-nucleotides. Nucleoside 5′-polyphosphates are high-energy phosphate esters, but are relatively unreactive in aqueous solution. This may be advantageous for enzyme-catalyzed polymerization, but is a severe obstacle for the nonenzymatic polymerization of nucleoside 5′-polyphosphates, which would occur far more slowly than the hydrolysis of the resulting polynucleotide.

In a different approach to the activation of nucleotides, the isolation of an activated intermediate is avoided by using a condensing agent such as a carbodiimide (Khorana 1961). This is a popular method in organic synthesis, but its application to prebiotic chemistry is problematic. Potentially prebiotic molecules such as cyanamide and cyanoacetylene activate nucleotides in aqueous solution, but the subsequent condensation reactions are inefficient (Lohrmann and Orgel 1973).

Most attempts to study nonenzymatic polymerization of nucleotides in the context of prebiotic chemistry have used nucleoside 5′-phosphoramidates, particularly nucleoside 5′-phosphorimidazolides. Although phosphorimidazolides can be formed from imidazoles and nucleoside 5′-polyphosphates (Lohrmann 1977), they are only marginally plausible as prebiotic molecules. They were chosen because they are prepared easily and react at a convenient rate in aqueous solution.

Nucleotides contain three principal nucleophilic groups: the 5′-phosphate, the 2′-hydroxyl, and the 3′-hydroxyl group, in order of decreasing reactivity. The reaction of a nucleotide or oligonucleotide with an activated nucleotide, therefore, normally yields 5′,5′-pyrophosphate-, 2′,5′-phosphodiester-, and 3′,5′-phosphodiester-linked adducts ( Fig. 1 A), in order of decreasing abundance (Sulston et al. 1968). Thus the condensation of several monomers would likely yield an oligomer containing one pyrophosphate and a preponderance of 2′,5′-phosphodiester linkages ( Fig. 1 B). There is little chance of producing entirely 3′,5′-linked oligomers from activated nucleotides unless a catalyst can be found that increases the proportion of 3′,5′-phosphodiester linkages. Several metal ions, particularly Pb 2+ and UO2 2+ , catalyze the formation of oligomers from nucleoside 5′-phosphorimidazolides (Sleeper and Orgel 1979 Sawai et al. 1988). The Pb 2+ -catalyzed reaction is especially efficient when performed in eutectic solutions of the activated monomers (in concentrated solutions obtained by partial freezing of more dilute solutions). Substantial amounts of long oligomers are formed under eutectic conditions, but the product oligomers always contain a large proportion of 2′,5′-linkages (Kanavarioti et al. 2001 Monnard et al. 2003).

Phosphodiester linkages resulting from chemical condensation of nucleotides. (A) Reaction of an activated mononucleotide (Ni+1) with an oligonucleotide (N1–Ni ) to form a 3′,5′-phosphodiester (left), 2′,5′-phosphodiester (middle), or 5′,5′-pyrophosphate linkage (right). (B) Typical oligomeric product resulting from chemical condensation of activated mononucleotides.

What kinds of prebiotically plausible catalysts might lead to the production of 3′,5′-linked oligonucleotides directly from nucleoside 5′-phosphorimidazolides or other activated nucleotides? It is unlikely, but not impossible, that a metal ion or simple acid-base catalyst would provide sufficient regiospecificity. The most attractive of the other hypotheses is that adsorption to a specific surface of a mineral might orient activated nucleotides rigidly and thus catalyze a highly regiospecific reaction.

The work of Ferris and coworkers provides support for this hypothesis (Ferris et al. 2004 Ferris 2006). They have studied the oligomerization of nucleoside 5′-phosphorimidazolides and related activated nucleotides on the clay mineral montmorillonite (Ferris and Ertem 1993 Kawamura and Ferris 1994 Miyakawa and Ferris 2003). Some samples of the mineral are effective catalysts, promoting the formation of oligomers even from dilute solutions of activated nucleotide substrates. Furthermore, the mineral profoundly affects the regiospecificity of the reaction. The oligomerization of adenosine 5′-phosphorimidazolide, for example, gives predominantly 3′,5′-linked products in the presence of montmorillonite, but predominantly 2′,5′-linked products in aqueous solution (Ding et al. 1996 Kawamura and Ferris 1999). Once short oligomers have been synthesized, they can be further extended by adsorbing them on either montmorillonite or hydroxylapatite and repeatedly adding activated monomers, resulting in the accumulation of mainly 3′,5′-linked oligoadenylates up to 40� subunits in length (Ferris et al. 1996 Ferris 2002). However, even when adsorbed on montmorillonite, the phosphorimidazolides of the pyrimidine nucleosides yield oligomers that are predominantly 2′,5′-linked.

Long oligomers have also been obtained from monomers in a single step using a different activated nucleotide in which imidazole is replaced by 1-methyl-adenine (Prabahar and Ferris 1997 Huang and Ferris 2003). Using the 1-methyl-adenine derivative of adenylate or uridylate, oligomers containing up to 40 subunits were produced, consisting of �% 3′,5′-linkages for oligoadenylate and �% 3′,5′-linkages for oligouridylate (Huang and Ferris 2006). Oligomerization of the 1-methyl-adenine derivative of guanylate or cytidylate was less efficient, but all four activated monomers could be co-incorporated, to at least a modest extent, within abiotically synthesized oligonucleotides.

Detailed analysis of this work on catalysis by montmorillonite suggests that oligomerization occurs at a limited number of structurally specific active sites within the interlayers of the clay (Wang and Ferris 2001). These sites must not be saturated with sodium ions, which appear to block access of the activated nucleotides (Joshi et al. 2009). Several different samples of montmorillonite have proven to be good catalysts, in part depending on their proton versus sodium ion content. It will be important to determine if there are other types of minerals that are comparably efficient catalysts of oligonucleotide synthesis, and if so, to study the regiospecificity and sequence generality of the reactions they catalyze.

2.2. Nonenzymatic Replication of RNA

If a mechanism existed on the primitive Earth for the polymerization of activated nucleotides, it would have generated a complex mixture of product oligonucleotides that differed in both length and sequence. The next stage in the emergence of an RNA World would have been the replication of some of these molecules, so that a process equivalent to natural selection could begin. The reaction central to replication of nucleic acids is template-directed synthesis, that is, the synthesis of a complementary oligonucleotide under the direction of a preexisting oligonucleotide. A good deal of work has already been performed on this aspect of nonenzymatic replication. This work has been reviewed elsewhere (Joyce 1987 Orgel 2004a), so only a summary of the results will be given here.

The first major conclusion is that most activated nucleotides do not undergo efficient, regiospecific, template-directed reactions in the presence of an RNA or DNA template. In general, only a small proportion of template molecules succeed in directing the synthesis of a complete complement, and the complement usually contains a mixture of 2′,5′- and 3′,5′-phosphodiester linkages. After a considerable search, a set of activated nucleotides was found that undergo efficient and highly regiospecific template-directed reactions. Working with guanosine 5′-phospho-2-methylimidazolide (2-MeImpG), it was shown that poly(C) can direct the synthesis of long oligo(G)s in a reaction that is highly efficient and highly regiospecific (Inoue and Orgel 1981). If poly(C) is incubated with an equimolar mixture of the four 2-MeImpNs (N = G, A, C, or U), less than 1% of the product consists of noncomplementary nucleotides (Inoue and Orgel 1982). Subsequent experiments suggested that this and the related reactions discussed later occur preferentially within the context of double helices that have a structure resembling the A form of RNA (Kurz et al. 1997, 1998 Kozlov et al. 1999, 2000).

Random copolymers containing an excess of C residues can be used to direct the synthesis of products containing G and the complements of the other bases present in the template (Inoue and Orgel 1983). The reaction with a poly(C,G) template is especially interesting because the products, like the template, are composed entirely of C and G residues. If these products in turn could be used as templates, it might allow the emergence of a self-replicating sequence. Self-replication, however, is unlikely, mainly because poly(C,G) molecules that do not contain an excess of C residues tend to form stable self-structures that prevent them from acting as templates (Joyce and Orgel 1986). The self-structures are of two types: (1) the standard Watson-Crick variety based on C•G pairs, and (2) a quadrahelix structure that results from the association of four G-rich sequences. As a consequence, any C-rich oligonucleotide that can serve as a good template will give rise to G-rich complementary products that tend to be locked in self-structure and so cannot act as templates. Overcoming the self-structure problem using the standard C and G nucleotides is very difficult because it requires the discovery of conditions that favor the binding of mononucleotides to allow template-directed synthesis to occur, but suppress the formation of long duplex regions that would exclude activated monomers from the template.

Some progress has been made in discovering defined-sequence templates that are copied faithfully to yield complementary products (Inoue et al. 1984 Acevedo and Orgel 1987 Wu and Orgel 1992a). Successful templates typically contain an excess of C residues, with A and U residues isolated from each other by at least three C residues. Runs of G residues are copied into runs of C residues, so long as the formation of self-structures by G residues can be avoided (Wu and Orgel 1992b). In light of the available evidence, it seems unlikely that a pair of complementary sequences can be found, each of which facilitates the synthesis of the other using nucleoside 5′-phospho-2-methylimidazolides as substrates. Some of the obstacles to self-replication may be attributable to the choice of reagents and reaction conditions, but others seem to be intrinsic to the template-directed condensation of activated mononucleotides.

A related nonenzymatic replication scheme involves synthesis by the ligation of short 3′,5′-linked oligomers (James and Ellington 1999). This is certainly an attractive possibility, made more plausible by the discovery of analogous ribozyme-catalyzed reactions (Bartel and Szostak 1993), but it faces two major obstacles. The first is the difficulty of obtaining the substrates in the first place. The second is concerned with fidelity. Pairs of oligonucleotides containing a single base mismatch, particularly if the mismatch forms a G•U wobble pair, still hybridize as efficiently as fully complementary oligomers, except in a temperature range very close to the melting point of the perfectly paired structure. Maintaining fidelity would therefore be difficult under any plausible temperature regime.

Despite these problems, template-directed ligation of short oligonucleotides may be a viable alternative to the oligomerization of activated monomers. Ferris' work discussed above suggests that predominantly 3′,5′-linked oligonucleotides might form spontaneously from activated nucleotides on some variety of montmorillonite (Ferris et al. 1996) or on some other mineral. Oligonucleotide 5′-triphosphates undergo slow but remarkably 3′,5′-regiospecific ligation in the presence of a complementary template (Rohatgi et al. 1996a,b). The combination of some such pair of reactions might provide a replication scheme for polynucleotides starting with an input of activated monomers.

There also are efforts in what is sometimes termed “synthetic biology” to achieve nonenzymatic replication with molecules that resemble biological nucleic acids, but are not constrained by considerations of plausible prebiotic chemistry. For example, the 2′- and 3′-hydroxyl groups of activated mononucleotides can be replaced by an amino group at either position, providing enhanced nucleophilicity and resulting in more rapid template-dependent (and template-independent) oligomerization (Lohrmann and Orgel 1976 Zielinski and Orgel 1985). Dinucleotide building blocks, consisting of 3′-amino, 3′-deoxynucleotide analogs can also be oligomerized in the presence of a suitable condensing agent (Zielinski and Orgel 1987). With additional modification of the nucleotide bases, it has been possible to carry out the template-directed copying of nucleic acid sequences that contain of all four bases (Schrum et al. 2009). These efforts, although not explaining the origin of the RNA World, contribute to understanding the chemical challenges that must be overcome in achieving the nonenzymatic replication of RNA.

2.3. The First RNA Replicase

The notion of the RNA World places emphasis on an RNA molecule that catalyzes its own replication. Such a molecule must function as an RNA-dependent RNA polymerase, acting on itself (or copies of itself) to produce complementary RNAs, and acting on the complementary RNAs to produce additional copies of itself. The efficiency and fidelity of this process must be sufficient to produce viable “progeny” RNA molecules at a rate that exceeds the rate of decomposition of the “parents.” Beyond these requirements, the details of the replication process are not highly constrained.

The RNA-first view of the origin of life assumes that a supply of activated ß- d -nucleotides was available by some as yet unrecognized abiotic process. Furthermore, it assumes that a means existed to convert the activated nucleotides to an ensemble of random-sequence polynucleotides, a subset of which had the ability to replicate. It seems to be implicit in the model that such polynucleotides replicate themselves but, for whatever reason, do not replicate unrelated neighbors. It is not clear whether replication involves one molecule copying itself (and its complement) or a family of molecules that together copy each other. These questions are set aside for the moment in order to first consider the question of whether an RNA molecule of reasonably short length can catalyze its own replication with sufficiently high fidelity.

Accuracy and Survival

The concept of an error threshold, that is, an upper limit to the frequency of copying errors that can be tolerated by a replicating macromolecule, was first introduced by Eigen (1971). This important idea has been extended in a series of mathematically sophisticated papers by McCaskill, Schuster, and others (McCaskill 1984a Eigen et al. 1988 Schuster and Swetina 1988). Here only a brief summary of the subject is provided.

Eigen's model (1971) envisages a population of replicating polynucleotides that draw on a limited supply of activated mononucleotides to produce additional copies of themselves. In this model, the rate of synthesis of new copies of a particular replicating RNA is proportional to its concentration, resulting in autocatalytic growth. The net rate of production is the difference between the rate of formation of error-free copies and the rate of decomposition of existing copies of the RNA. For an advantageous RNA to outgrow its competitors, its net rate of production must exceed the mean rate of production of all other RNAs in the population. Only the error-free copies of the advantageous RNA contribute to its net rate of production, but all the copies of the other RNAs contribute to their collective production. Thus the relative advantage enjoyed by the advantageous individual compared with the rest of the population (often referred to as the “superiority” of the advantageous individual) must exceed the probability of producing an error copy of that advantageous individual.

The proportion of copies of an RNA that are error free is determined by the fidelity of the component condensation reactions that are required to produce a complete copy. For simplicity, consider a self-replicating RNA that is formed by n condensation reactions, each having mean fidelity q. The probability of obtaining a completely error-free copy is given by q n , which is the product of the fidelity of the component condensation reactions. If an advantageous individual is to outgrow its competitors, q n must exceed the superiority, s, of that individual. Expressed in terms of the number of reactions required to produce the advantageous individual,

For s > 1 and q > 0.9, this equation simplifies to

This is the 𠇎rror threshold,” which describes the inverse relationship between the fidelity of replication, q, and the maximum allowable number of component condensation reactions, n. The maximum number of component reactions is highly sensitive to the fidelity of replication, but depends only weakly on the superiority of the advantageous individual. For a self-replicating RNA that is formed by the template-directed condensation of activated mononucleotides, a total of 2n – 2 condensation reactions are required to produce a complete copy. This takes into account the synthesis of both a complementary strand and a complement of the complement.

It should be recognized that a marked superiority of one sequence over all other sequences could not be maintained over evolutionary time because novel variants would soon arise to challenge the dominant species. However, a marked initial superiority may be important in allowing an efficient self-replicating RNA to emerge from a pool of less efficient replicators. In the absence of other efficient replicators, a primitive self-replicating RNA that operates with low fidelity may gain a foothold by taking advantage of a somewhat less stringent error threshold. Whether or not this can occur depends on its superiority. For example, an RNA that replicates 10-fold more efficiently than its competitors and does so with 90% fidelity could be no longer than 12 nucleotides, and a similarly advantageous RNA that replicates with 70% fidelity could be no longer than four nucleotides. It seems highly unlikely than any of the 17 million possible RNA dodecamers is able to catalyze its own replication with 90% fidelity, and even less likely that a tetranucleotide could catalyze its own replication with 70% fidelity. However, an RNA that replicates 10 6 -fold more efficiently than its competitors and does so with 90% fidelity could be as long as 67 nucleotides, and one that replicates with 70% fidelity could be as long as 20 nucleotides.

When self-replication is first established, fidelity is likely to be poor and there is strong selection pressure favoring improvement of the fidelity. As fidelity improves, a larger genome can be maintained. This allows exploration of a larger number of possible sequences, some of which may lead to further improvement in fidelity, which in turn allows a still larger genome size, and so on. Once the evolving population has achieved a fidelity of about 99%, a genome length of about 100 nucleotides can be maintained, even for modest superiority values. This would allow RNA-based life to become firmly established. Until that time, it is a race between evolutionary improvement in the context of a sloppy self-replicating system and the risk of delocalization of the genetic information because of overstepping the error threshold. If the time required to bootstrap to high fidelity and large genomes is too long, there is a risk that the population will succumb to an environmental catastrophe before it has had the chance to develop appropriate countermeasures.

It is difficult to state with certainty the minimum possible size of an RNA replicase ribozyme. An RNA consisting of a single secondary structural element, that is, a small stem-loop containing 12� nucleotides, would not be expected to have replicase activity, whereas a double stem-loop, perhaps forming a 𠇍umbbell” structure or a pseudoknot, might just be capable of a low level of activity. A triple stem-loop structure, containing 40� nucleotides, offers a reasonable hope of functioning as a replicase ribozyme. One could, for example, imagine a molecule consisting of a pseudoknot and a pendant stem-loop that forms a cleft for template-dependent replication.

Suppose there is some 40-mer that enjoys a superiority of 10 3 -fold and replicates with 90% fidelity. This should be regarded as a highly optimistic but not outrageous view of what is possible for a minimum replicase ribozyme. Would such a molecule be expected to occur within a population of random-sequence RNAs? A complete library consisting of one copy each of all 10 24 possible 40-mers would weigh about 1 kg. There may be many such 40-mers, encompassing both distinct structural motifs and, more importantly, a large number of equivalent representations of each motif. As a result, even a small fraction of the total library, consisting of perhaps 10 20 sequences and weighing about 1 g, might be expected to contain at least one self-replicating RNA with the requisite properties. It is not sufficient, however, that there be just one copy of a self-replicating RNA. The above calculations assume that a self-replicating RNA can copy itself (or that a fully complementary sequence is automatically available, as will be discussed later). If two or more copies of the same 40mer RNA are needed, then a much larger library, consisting of 10 48 RNAs and weighing 10 28 g would be required. This amount is comparable to the mass of the Earth.

At first sight, it might seem that one way to ease the error threshold would be for the replicase ribozyme to accept dinucleotide or trinucleotide substrates, so that copies of the RNA could be formed by fewer condensation reactions. Calculations show that, over a broad range of superiority values, RNAs that are required to replicate with 90% fidelity when using mononucleotide substrates would be required to replicate with roughly 80% fidelity when using dinucleotide substrates or roughly 70% fidelity when using trinucleotide substrates. Thus the use of short oligomers offers only a modest advantage because of lessening of the error threshold, which likely would be outweighed by the greater difficulty of achieving high fidelity when discriminating among the 16 possible dinucleotide or 64 possible trinucleotide substrates, rather than among the four mononucleotides.

If one accepts the RNA-first view that there was a prebiotic pool of random-sequence RNAs, and if one assumes that the pool included a replicase ribozyme containing, say, 40 nucleotides and replicating itself with about 90% fidelity, then it is not difficult to imagine how RNA-based evolution might have started. During the initial period a successful clone would have expanded in the absence of competition. As competition for substrates intensified there would have followed a succession of increasingly more advantageous individuals, each replicating within its error threshold. After a period of intensifying competition, the single most advantageous species would have been replaced by a “quasispecies,” that is, a mixture of the most advantageous individual and substantial amounts of closely related individuals that replicate almost as fast and almost as faithfully as the most advantageous one (Eigen and Schuster 1977 Eigen et al. 1988). Under these conditions the persistence of a particular advantageous individual is no longer the problem, but one must understand the evolution of the composition of the quasispecies and the conditions for its persistence. This difficult problem has been partially solved by McCaskill (1984b). The general form of the solution is very similar to the error threshold described by Eigen (1971), but with different values for the constant in the inequality. Thus concerns about the error threshold apply to the quasispecies as well as to the succession of individuals. Practically speaking, however, once a quasispecies distribution of sophisticated replicators had emerged, the RNA World would have been on solid footing and, barring an environmental catastrophe, unlikely to lose the ability to maintain genetic information over time.

Another Chicken-and-Egg Paradox

The previous discussion has tried mightily to present the most optimistic view possible for the emergence of an RNA replicase ribozyme from a soup of random-sequence polynucleotides. It must be admitted, however, that this model does not appear to be very plausible. The discussion has focused on a straw man: The myth of a small RNA molecule that arises de novo and can replicate efficiently and with high fidelity under plausible prebiotic conditions. Not only is such a notion unrealistic in light of current understanding of prebiotic chemistry (Joyce 2002), but it should strain the credulity of even an optimist's view of RNA's catalytic potential. If you doubt this, ask yourself whether you believe that a replicase ribozyme would arise in a solution containing nucleoside 5′-diphosphates and polynucleotide phosphorylase!

If one accepts the notion of an RNA World, one is faced with the dilemma of how such a genetic system came into existence. To say that the RNA World hypothesis “solves the paradox of the chicken-and-the-egg” is correct if one means that RNA can function both as a genetic molecule and as a catalyst that promotes its own replication. RNA-catalyzed RNA replication provides a chemical basis for Darwinian evolution based on natural selection. Darwinian evolution is a powerful way to search among vast numbers of potential solutions for those that best address a particular problem. Selection based on inefficient RNA replication, for example, could be used to search among a population of RNA molecules for those individuals that promote improved RNA replication. But here one encounters another chicken-and-egg paradox: Without evolution it appears unlikely that a self-replicating ribozyme could arise, but without some form of self-replication there is no way to conduct an evolutionary search for the first, primitive self-replicating ribozyme.

One way that RNA evolution may have gotten started without the aid of an evolved catalyst might be by using nonenzymatic template-directed synthesis to permit some copying of RNA before the appearance of the first replicase ribozyme. Suppose that the initial ensemble of monomers was not produced by random copolymerization, but rather by a sequence of untemplated and templated reactions ( Fig. 2 ), and further suppose that members of the initial ensemble of multiple stem-loop structures could be replicated, albeit inefficiently, by the template-directed process. This would have two important consequences. First, any molecule with replicase function that appeared in the mixture would likely find in its neighborhood similar molecules and their complements, related by descent, thus eliminating the requirement for two unrelated replicases to meet. Second, a majority of molecules in the mixture would contain stem-loop structures. If it is true that ribozyme function is favored by stable self-structure, and if the base-sequences of the stems in stem-loop structures are relatively unimportant for function, this model might provide an economical way of generating a relatively small ensemble of sequences that is enriched with catalytic sequences.

Nonenzymatic synthesis of multi-stem-loop structures as a result of untemplated (open arrowhead) and templated (filled arrowhead) reactions. Template-directed synthesis is assumed to occur rapidly whenever a template, activated monomers, and a suitable primer are available. Once the complementary strand is completed, additional residues are added slowly in a random-sequence manner.

How plausible is the assumption that replicases could act on sequences similar to themselves, while ignoring unrelated sequences? This selectivity could be ensured by segregating individual molecules (or clonal lines) on the surface of mineral grains, on the surface of micelles, or within membranes. Closely related molecules might be segregated as a group through specific hydrogen-bonding interactions (the family that sticks together, replicates together). For any segregation mechanism, weak selection would result if the replicating molecules are sufficiently dispersed that diffusion over their intermolecular distance is slow compared with replication. Computer simulations have shown that under such conditions of segregation, evolutionary bootstrapping can occur, resulting in progressively larger genomes that are copied with progressively greater fidelity (Szabó et al. 2002). Alternatively, the requirement for replication of related, but not unrelated, sequences might be met through the use of “genomic tags” (Weiner and Maizels 1987). Among self-replicating sequences, it is plausible that some are restricted to copying molecules with a particular 3′-terminal subsequence. A replicator that happened by chance to carry a terminal sequence that matched the preference of its active site would replicate itself while ignoring its neighbors.

Another resolution of the paradox of how RNA evolution was initiated without the aid of an evolved ribozyme is to abandon the RNA-first view of the origin of life and suppose that RNA was not the first genetic molecule (Cairns-Smith 1982 Shapiro 1984 Joyce et al. 1987 Joyce 1989, 2002 Orgel 1989, 2004a). Perhaps RNA replication arose in the context of an evolving system based on something other than RNA (see the section 𠇊lternative Genetic Systems”). Even if this is true, all of the arguments concerning the relationship between the fidelity of replication and the maximum allowable genome length would still apply to this earlier genetic system. Of course, the challenge to those who advocate the RNA-later approach is to show that there is an informational entity that is prebiotically plausible and is capable of initiating its own replication without the aid of a sophisticated catalyst.

2.4. Replicase Function in the Evolved RNA World

Although it is difficult to say how the first RNA replicase ribozyme arose, it is not difficult to imagine how such a molecule, once developed, would function. The chemistry of RNA replication would involve the template-directed polymerization of mono- or short oligonucleotides, using chemistry in many ways similar to that used by contemporary group I ribozymes (Cech 1986 Been and Cech 1988 Doudna and Szostak 1989). One important difference is that, unlike group I ribozymes, which rely on a nucleoside or oligonucleotide leaving group, an RNA replicase would more likely make use of a different leaving group that provides a substantial driving force for polymerization and that, after its release, does not become involved in some competing phosphoester transfer reaction.

From Ligases to Polymerases

The polymerization of activated nucleotides proceeds via nucleophilic attack by the 3′-hydroxyl of a template-bound oligonucleotide at the α-phosphorus of an adjacent template-bound nucleotide derivative ( Fig. 3 ). The nucleotide is �tivated” for attack by the presence of a phosphoryl substituent, for example a phosphate, polyphosphate, alkoxide, or imidazole group. As discussed previously, polyphosphates, such as inorganic pyrophosphate, are the most obvious candidates for the leaving group. The condensation reaction could be assisted by favorable orientation of the reactive groups, deprotonation of the nucleophilic 3′-hydroxyl, stabilization of the trigonal-bipyramidal transition state, and charge neutralization of the leaving group. All of these tasks might be performed by RNA (Narlikar and Herschlag 1997 Emilsson et al. 2003), acting either alone (Ortoleva-Donnelly and Strobel 1999) or with the help of a suitably positioned metal cation or other cofactor (Shan et al. 1999 Shan et al. 2001).

Nucleophilic attack by the 3′-hydroxyl of a template-bound oligonucleotide (N1–Ni) on the α-phosphorus of an adjacent template-bound mononucleotide (Ni+1). Dotted lines indicate base pairing to a complementary template. R is the leaving group.

The possibility that an RNA replicase ribozyme could have existed has been made abundantly clear by work involving ribozymes that have been developed in the laboratory through in vitro evolution (Bartel and Szostak 1993 Ekland et al. 1995 Ekland and Bartel 1996 Robertson and Ellington 1999 Jaeger et al. 1999 Rogers and Joyce 2001 Johnston et al. 2001 McGinness and Joyce 2002 Ikawa et al. 2004 Fujita et al. 2009). Bartel and Szostak (1993), for example, began with a large population of random-sequence RNAs and evolved the 𠇌lass I” RNA ligase ribozyme, an optimized version of which is about 100 nucleotides in length and catalyzes the joining of two template-bound oligonucleotides. Condensation occurs between the 3′-hydroxyl of one oligonucleotide and the 5′-triphosphate of another, forming a 3′,5′-phosphodiester linkage and releasing inorganic pyrophosphate. This reaction is classified as ligation because of the nature of the oligonucleotide substrates, but involves the same chemical transformation as is catalyzed by modern RNA polymerase enzymes.

X-ray crystal structures of two RNA ligase ribozymes, the L1 and above-mentioned class I ligases, have been determined, providing a glimpse into the mechanistic strategies that these two structurally and evolutionarily distinct ribozymes use to catalyze the same reaction (Robertson and Scott 2007 Shechner et al. 2009) ( Fig. 4 ). Both crystal structures capture the product of the ligation reaction, and consequently offer an incomplete view of the reaction pathway. For example, the pyrophosphate leaving group is absent from the structures, so no conclusions can be drawn regarding potential ribozyme-assisted orientation of the reactive triphosphate or charge neutralization of the pyrophosphate leaving group. There is, however, information regarding other aspects of the reaction mechanism that can be inferred from the product structures.

X-ray crystal structure of the (A) L1 ligase and (B) class I ligase ribozymes. Insets show the putative magnesium ion binding sites at the respective ligation junctions. The structures are rendered in rainbow continuum, with the 5′-triphosphate-bearing end of the ribozyme colored violet and the 3′-hydroxyl-bearing end of the substrate colored red. The phosphate at the ligation junction is shown in white, and the proximate magnesium ion (modeled for the class I ligase) is shown as a yellow sphere, with dashed lines indicating coordination contacts.

Both the L1 and class I ligases are dependent on the presence of magnesium ions for their activity. A prominent feature of the L1 structure ( Fig. 4 A) involves a bound metal ion in the active site, coordinated by three nonbridging phosphate oxygens, one of which belongs to the newly formed phosphodiester linking what originally were the two substrates. This magnesium ion is favorably positioned to help neutralize the increased negative charge of the transition state and, potentially, to activate the 3′-hydroxyl nucleophile and to help orient the α-phosphate for a more optimal in-line alignment. In the case of the class I structure ( Fig. 4 B), no catalytic metal ions appear to have been retained in the vicinity of the active site, although two magnesium ions are observed to participate in crucial structural interactions that help shape the active site architecture. Despite the lack of direct observation of a catalytic metal at the active site, there is what appears to be an empty metal binding site formed by two nonbridging phosphate oxygens, positioned directly opposite the ligation junction in a manner similar to that observed for the magnesium binding site of the L1 ligase and reminiscent of the arrangement seen in protein polymerases. The lack of a metal in the crystal structure may simply be an artifact of the crystallization process or may imply a local conformational change in the product that disfavors retention of the bound metal. These structures show that, despite some remaining gaps in the detailed understanding of how these ribozymes function, the available information points to a universal catalytic strategy, very similar to that used by modern protein-based RNA polymerases.

Subsequent to its isolation as a ligase, the class I ribozyme was shown to catalyze a polymerization reaction in which the 5′-triphosphate-bearing oligonucleotide is replaced by one or more NTPs (Ekland and Bartel 1996). This reaction proceeds with high fidelity (q = 0.92), but the reaction rate drops sharply with successive nucleotide additions.

Bartel and colleagues performed further in vitro evolution experiments to convert the class I ligase to a bona fide RNA polymerase that operates on a separate RNA template (Johnston et al. 2001). To the 3′ end of the class I ligase they added 76 random-sequence nucleotides that were evolved to form an accessory domain that assists in the polymerization of template-bound NTPs. The polymerization reaction is applicable to a variety of template sequences, and for well-behaved sequences proceeds with an average fidelity of 0.967. This would be sufficient to support a genome length of about 30 nucleotides, although the ribozyme itself contains about 190 nucleotides. The ribozyme has a catalytic rate for NTP addition of at least 1.5 min 𢄡 , but its Km is so high that, even in the presence of micromolar concentrations of oligonucleotides and millimolar concentrations of NTPs, it requires about 2 h to complete each NTP addition (Lawrence and Bartel 2003). The ribozyme operates best under conditions of high Mg 2+ concentration, but becomes degraded under those conditions over 24 h, by which time it has added no more than 14 NTPs (Johnston et al. 2001).

Further optimization of the polymerase ribozyme using highly sophisticated in vitro evolution techniques has led to additional improvements in its biochemical properties. By directly selecting for extension of an external primer on a separate template, Zaher and Unrau (2007) were able to improve the maximum length of template-dependent polymerization to 㸠 nucleotides, with a rate that is ∼threefold faster than that of the parent for the first nine monomer additions and up to 75-fold faster for additions beyond 10 nucleotides. In addition, although not rigorously quantitated, the new ribozyme displays significantly improved fidelity, particularly with respect to discrimination against G•U wobble pairs. It is this improved fidelity that appears to be the underlying source for the observed improvements in the maximum length of extension and the rate of polymerization.

A different RNA ligase ribozyme can operate on a separate RNA template in a largely sequence-general manner, and does so with a Km that is at least 100-fold lower than that of the class-I-derived polymerase (McGinness and Joyce 2002). However, its catalytic rate is much lower as well, and it is unable to add more than a single NTP. Yet another RNA ligase ribozyme can operate on a separate template with the help of designed tertiary interactions that 𠇌lamp” the template–substrate complex to the ribozyme (Ikawa et al. 2004). But it too is a relatively slow catalyst that cannot add more than a single NTP.

A highly pessimistic view is that because there is no known polymerase ribozyme that combines all of the properties necessary to sustain its own replication, no such ribozyme is possible. A more balanced view is that RNA clearly is capable of greatly accelerating the template-dependent polymerization of nucleoside 5′-polyphosphates. Such catalytic RNAs can operate in a sequence-general manner and with reasonable fidelity. It seems only a matter of time (and likely considerable effort) before more robust polymerase ribozymes will be obtained. Nature did not have the opportunity to conduct carefully arranged evolution experiments using highly-purified reagents, but did have the luxury of much greater reaction volumes and much more time.

RNA Replication

Despite falling short of the ultimate goal of a general-purpose RNA polymerase ribozyme, a robust reaction system for RNA-catalyzed RNA replication has recently been shown. The system uses a pair of cross-replicating ligase ribozymes that each catalyze the formation of the other, using a mixture of four different substrate oligonucleotides (Lincoln and Joyce 2009). In reaction mixtures containing only these RNA substrates, MgCl2, and buffer, a small starting amount of ribozymes gives rise to many additional ribozymes through a process of RNA-catalyzed exponential amplification. Whenever the substrates become depleted, the replication process can be restarted and sustained indefinitely by replenishing the supply of substrates.

Because the substrates are recognized by the ribozymes through specific Watson-Crick pairing interactions, evolution experiments can be performed by providing a variety of substrates that have different sequences in these recognition regions and different corresponding sequences in the catalytic domain of the ribozyme. RNA replication was performed with a library of 144 possible substrate combinations, resulting in the emergence of a set of highly advantageous replicators that included recombinants which were not present at the start of the experiment. Until the advent of a general-purpose RNA polymerase ribozyme, the system of cross-replicating ligases offers the best platform to study the biochemical properties and evolutionary behavior of an all-RNA replicative system.

Nucleotide Biosynthesis

RNA replicase activity is probably not the only catalytic behavior that was essential for the existence of the RNA World. Maintaining an adequate supply of the four activated nucleotides would have been a top priority. Even if the prebiotic environment contained a large reservoir of these compounds, the reservoir would eventually become depleted, and some capacity for nucleotide biosynthesis would have been required.

Ribozymes have been obtained, through in vitro evolution, that catalyze some of the steps of nucleotide biosynthesis. Unrau and Bartel (1998), for example, developed a ribozyme that catalyzes a reaction between 4-thiouracil and 5-phosphoribosyl-1-pyrophosphate (PRPP) to form 4-thiouridylate ( Fig. 5 A). The 4-thiouracil is provided free in solution and the PRPP is tethered to the 3′ end of the ribozyme. An optimized form of this ribozyme, containing 124 nucleotides, has an observed rate of 0.2 min 𢄡 in the presence of 4 mM 4-thiouracil (Chapple et al. 2003). This is at least 10 7 -fold faster than the uncatalyzed rate of reaction, which is too slow to measure. Unrau and colleagues used a similar approach to develop two different ribozymes that catalyze the formation of 6-thioguanylate from 6-thioguanine and tethered PRPP (Lau et al. 2004), as well as a third guanylate synthase ribozyme that arose as an unanticipated consequence of a related in vitro evolution experiment (Lau and Unrau 2009). The first two guanylate synthase ribozymes are slightly larger and have about twofold higher catalytic efficiency compared with the uridylate synthase ribozyme, although guanylate synthesis is expected to have a much higher uncatalyzed rate of reaction.

Known RNA-catalyzed reactions that are relevant to nucleotide biosynthesis. (A) Formation of 4-thiouridylate from free 4-thiouracil and ribozyme-tethered 5-phosphoribosyl-1-pyrophosphate. (B) 5′-phosphorylation of an oligonucleotide using γ-thio-ATP as the phosphate donor. (C) Activation of a nucleoside 5′-phosphate by formation of a 5′,5′-pyrophosphate linkage. (D) Template-directed ligation of RNA driven by release of a 5′,5′-pyrophosphate-linked adenylate.

RNA-catalyzed synthesis of PRPP has not been shown, but a ribozyme has been obtained that catalyzes the 5′-phosphorylation of oligonucleotides using γ-thio-ATP as the phosphate donor (Lorsch and Szostak 1994) ( Fig. 5 B). The ribozyme shows a rate enhancement of about 10 9 -fold compared with the uncatalyzed rate of reaction. Once a nucleoside 5′-phosphate has been formed, it canphosphoryl be activated by another ribozyme that catalyzes the condensation of a nucleoside 5′-phosphate and a ribozyme-tethered nucleoside 5′-triphosphate (Huang and Yarus 1997) ( Fig. 5 C). This results in the formation of a 5′,5′-pyrophosphate linkage, which provides an activated nucleotide leaving group that can drive subsequent RNA-catalyzed, template-directed ligation of RNA (Hager and Szostak 1997) ( Fig. 5 D).

None of these four RNA-catalyzed reactions has precisely the right format for the corresponding reaction in a hypothetical nucleotide biosynthesis pathway in the RNA World. However, they show that RNA is capable of performing the relevant chemistry with substantial catalytic rate enhancement. It remains to be seen whether ribozymes can be developed that catalyze the formation of the fundamental building blocks of RNA, d -ribose and the four nucleotide bases, using starting materials that would have been abundant on the primitive Earth.


Have Scientists Finally Created Life?

S upposedly scientists finally did it. “Scientists Create Synthetic Life in Lab” trumpeted the Associated Press. bbc News announced an “‘Artificial Life’ Breakthrough.” “Scientists Create First Self-Replicating Synthetic Life,” proclaimed Wired Science.

After more than a century of trial and error, scientists say they have finally created life. But have scientists really disproved the law of biogenesis? Can life come from something besides life? Can it come from a test tube?

On May 21, the Wall Street Journal said humankind has potentially entered a “new era in biology.” For the first time, scientists “have created a synthetic cell, completely controlled by man-made genetic instructions,” it reported.

“This is literally a turning point in the relationship between man and nature,” one molecular biologist said. “For the first time, someone has generated an entire artificial cell with predetermined properties.”

The project’s leader, Craig Venter, said, “These are very much real cells” while simultaneously being “pretty clearly human inventions.”

The scientists took the dna of a very simple, single-celled bacteria, Mycoplasma Capricolum. Using a computer, they deciphered the 1 million-plus combinations of the four molecules that make up its dna (cytosine, guanine, adenine, thymine).

The scientists then added laboratory-manufactured batches of those four molecules to yeast cells, stitching together an exact copy of Mycoplasma Capricolum’s dna . To prove they had created their own synthetic copy of the dna , Venter’s team added additional non-functional code to the bacteria’s genome. They wrote their names and a quote from poet James Joyce—“To live, to err, to fall, to triumph, to recreate life out of life”—into the genetic code.

They then removed the genetic material from a second, closely related species of bacteria and substituted the manufactured dna .

After multiple failures, the scientists finally induced the newly impregnated bacteria not only to grow, but reproduce. The new progeny cells took on the characteristics of the bacteria from which the dna was copied.

It was an amazing accomplishment to be sure. And after $40 million spent and 15 years of letdowns and failures (the experiment once failed because a single base pair out of the 1 million-plus had been incorrectly copied), you can understand why these scientists would be ecstatic.

And if this experiment is as significant as some claim, this sets a new level of human accomplishment. Already, big, moneyed defense contractors and oil companies are eager to take advantage of the new technology. Scientists claim that human-engineered organisms will someday be used to do everything from cleaning up oil spills and producing biofuel to making vaccines and capturing greenhouse gasses. Other scientists warn that the new technology portends another step toward human annihilation thanks to unbeatable biological weapons.

The White House got in on the action too. Last Thursday, President Obama asked the Presidential Commission for the Study of Bioethical Issues to study the implications of this “scientific milestone.”

But with all the hoopla surrounding the announcement, don’t overlook the facts. The scientists never actually created new life! They didn’t even get close.

First: The genetic code “created” by the scientists was really a copy of the code from an existing bacterium. There was nothing new about it. The scientists did add some additional material to the dna (their names and the quote), but it was useless material for the bacteria. It would be like a computer programmer inserting his favorite movie quote, or his birth date into a software code. It is there, but it does nothing.

Second: The copied dna was inserted into another living bacteria. The scientists did not “create” any of the organelles—the cell membrane, the cytoplasm, etc.—of that second bacteria either.

So what exactly did the scientists actually create?

Nothing. They copied, they manipulated, they forced nature in unnatural ways, but they did not create life!

The law of biogenesis still stands! Life can only come from life.

Life can’t come from dead materials. In fact, it can’t even be created when a team of intelligent designers with supercomputers and millions of dollars take living materials and try to stitch together a Little Frankenstein.

From the time of Louis Pasteur and Francesco Redi, scientists have known that life can only come from life. It is enshrined in the rarest of all scientific classifications: a law. And it’s one that plagues evolutionists.

In an effort to support the theory of evolution, scientists have been trying to conceive of some way that life could spontaneously generate from inorganic, non-living materials. (And don’t even ask where the materials came from.) Just accept that there was a primordial soup of water and chemicals that existed on Earth billions of years ago. At some point, for some unknown reason—a lightning bolt or a volcanic eruption, or just blind chance—caused the chemicals to unite into a living organism that could capture energy, grow, and reproduce itself. Supposedly, over billions of years, this organism not only survived subsequent volcanoes and lightning bolts, but—perhaps millions of years later—accidentally mutated its accidentally created genetic code in accidentally positive ways—millions and billions of times over—until eventually humans and billions of other incredibly diverse, interrelated, durable, thriving organisms came into being—for no other reason than to live and then die.

Look at the herculean effort it took for the scientists to just learn how to copy existing dna of one of the most simple, tiny, single-celled organisms, and get it to work in another virtually identical cell.

This one team alone spent 15 years of daily work, using the most advanced technology available in an ideal, controlled, laboratory environment, and taking advantage of highly refined, specific, reverse-engineered chemicals provided by scientists working at other companies. And all that effort and understanding was made possible by the work and discovery of centuries of other scientists before them.

The bacteria cell the scientists worked on had one chromosome. Humans have 46 chromosomes. There are some plants on Earth that have more than 1,000 chromosomes. And what happened when the scientists got just one letter of the 1 million-plus codes on the dna chromosome wrong? The cell died. There was no reproduction. There was no life.

Ask any computer programmer what happens when he accidentally writes one bad letter into his code.

There are millions, perhaps billions of computers on this Earth. How many times have you heard of computer software mutating—and something good resulting?

But even if a line of computer code did randomly mutate and produce something unexpectedly beneficial, what are the odds that another beneficial mutation would occur? And then again and again—billions of times over until the computer became not only a smarter computer, but an automobile or a nuclear aircraft carrier?

And what are the odds it would be a bundle of unreadable mess?

Yet evolutionists would have you believe that life—with all of its intricacy—could spring into existence from non-living compounds and then begin reproducing and randomly mutating into more advanced organisms.

As James Joyce said: “To live, to err, to fall, to triumph, to recreate life out of life.”


Solutions or merely thought experiments?

Secularists will avoid the discussion of abiogenesis because it is largely a black-box and they have no real answers for it. Rather they begin their version of the evolutionary continuum at the first replicating organism [7] [8] [9] which they freely confess is a very complex organism. It must at a minimum: replicate, absorb food, dispose of waste and produce power. This last function, to produce power, is the ATP "currency of life" found in every living cell on Earth. The ATP Synthase Motor [10] is a complex molecular motor measuring less than 40nm across.

While many creationists may engage a discussion on evolution with a secularist in terms of "molecules-to-man", the evolutionary thinker will significantly shorten this timeframe and begin with the "first replicating genome". This amounts to no more than a front-loaded thought-experiment, not a product of scientific integrity. Anyone can stand on the shoulders of genius and claim victory. That the secularist uses this thought-experiment as a starting point is arbitrarily inconsistent. They are essentially admitting that the origin of life is too complex to discuss and that the evolutionary narrative must be front-loaded with a complex life form. The question is not where did this life form come from but rather why do you think such imaginative fables are actually science?

There remains no known process acting in nature to produce life from non-life, therefore, abiogenesis exists out of the realm of empirical science. Furthermore, the extreme complexity of all lifeforms seems to point in the direction of an established Intelligence outside of nature. The Intelligence designed life to be governed by what are observed natural mechanisms or processes that enable diversity. This is perhaps why Francis Crick (one of the Discoverers of DNA) and Leslie Orgel (a microbiologist) proposed the theory of directed panspermia: the belief that life came to earth from outer space. The origin of life conundrum has scientists theorizing that life might have begun on some other planet (See: Panspermia). The theory is currently experiencing a revival and much of the research currently underway by NASA is an attempt to discover signs of life on other planets, such as Mars.

However, if microbes (or evidence of microbes) are found in space, this is not evidence of life outside the Earth. During the Flood, it is presumed that the fountains of the great deep had enormous, explosive power and delivered a significant portion of the Earth's mass into outer space, potentially carrying microbes with it. A latent evidence of this loss-of-mass is the current rotation speed of the Earth, marking 365+ days per year. In the time before the Flood, Genesis 7,8 and 9 provide a detailed rundown of the days involved. We can count twelve months of thirty days each, for a grand total of 360 days. If the Earth lost significant mass in the Flood, this would reduce its total circumference and likewise increase its rotation speed (just as a figure skater may spin faster by retracting her arms). Just as all cultures worldwide adhere to a seven-day week, so also to all culture measure a circle in terms of 360 degrees. There is no astronomical or other objective reason to use either one. Clearly the seven-day week is a holdover from the original creation week, and 360 degrees for a circle is a holdover from the original pre-Flood calendar.