The Origin and Evolution of Life on Earth

“There is no fundamental difference between a living organism and lifeless matter. The complex combination of manifestations and properties so characteristic of life must have arisen in the process of the evolution of matter.”

Oparin, A.I. The Origin of Life, Foreign Languages Publishing House (1924) Dover publication (1938).

Spontaneous Generation?A 17th century recipe for the spontaneous generation of mice: • place sweaty underwear and

husks of wheat in an open-mouthed jar

• Wait 21 days while sweat from the underwear penetrates the husks of wheat and changes them into mice!

Although such a concept may seem laughable today, it was consistent with other widely held cultural and religious beliefs of the time and people believed it up through the 1900’s!

Pasteur Refutes Spontaneous Generation

Spontaneous generation was laid to rest in 1859 by Louis Pasteur.Pasteur boiled meat broth in a flask, heated the neck of the flask in a flame until it became pliable, and bent it into the shape of an S.

When Pasteur tilted the flask so that the broth reached the lowest point in the neck, where any airborne particles would have settled, the broth rapidly became cloudy with life. Pasteur had both refuted the theory of spontaneous generation and convincingly demonstrated that microorganisms are everywhere - even in the air.

Air could enter the flask, but airborne microorganisms could not - they would settle by gravity in the neck—no microorganisms grew.

Spontaneous Origin if LifeProbable or Improbable?

Suppose the spontaneous generation of life is a reasonably improbable event—say it has a chance of one in a million (10-6 / yr) of happening in any particular year.

Suppose, instead, that the probability of the spontaneous origin of life in any given year on Earth were one in a trillion, or 10-12 / yr.

In other words, this incredibly long time has transformed the event from one which is highly improbable to an event which is now almost inevitable!

But during the Earth’s lifetime, about 4.5 billion years, the chance that it will happen at least once is very close to one. How close? The chance per year that it doesn’t happen is 999,999/1,000,000. The chance that it doesn’t happen in 4.5 billion years is 0.999,999 4,500,000,000 = 0 to nine decimal places.

During a human lifetime, roughly 100 years, the chances of it happening would be quite small—about 10-6 per year x 102 years = 10-4.

The probability that life would arise on Earth at any time during its existence would now be about 10-12 per year x 4.5 x 109 years = 4.5 x 10-3, a very small number. If this were the case, we are here only through an extraordinary stroke of luck!

Tornedo in the JunkyardMany scientists have argued that the latter scenario is more likely. They base this supposition on a specious argument, such as calculating the probability of assembling a protein out of amino acids in a purely random fashion.

“The chance that higher life forms might have emerged in this way is comparable to the chance that a tornado sweeping through a junkyard might assemble a Boeing 747 from the materials therein.…Life as we know it is, among other things, dependent on at least 2000 different enzymes. How could the blind forces of the primal sea manage to put together the correct chemical elements to build enzymes?”

The distinguished astrophysicist, Fred Hoyle, estimated that the odds of cellular life arising were about one in 1040000! He commented…

Consider a protein consisting of 100 amino acids. Any ‘slot’ in the chain can be occupied by one of twenty possibilities. The random assembly of a particular amino acid sequence to form the protein has a probability of (1/20)100, or about 10 -130. The probability of randomly assembling all the other organic molecules that make up life boggles the mind!

What’s Wrong?Spontaneous generation of life was not a purely random process! Proteins, RNA, DNA and the other molecules of life did not suddenly form randomly out of molecular building blocks. Their formation is a function of the laws of chemistry and biochemistry. The process is decidedly not random. The formation was a multi-step process in which ever more complicated assemblages emerged from slightly simpler ones that preceded them, but there was a much less complex ‘first molecule’ which might be characterized as alive, even though its formation might be termed ‘an accident.’

The evolutionary biologist, Richard Dawkins says in “The Selfish Gene,” —“At some point a particular remarkable molecule was formed by accident. We will call it the Replicator. It may not necessarily have been the biggest or most complicated molecule around, but it had the extraordinary property of being able to make copies of itself. This may seem like a very unlikely sort of accident to happen. So it was. It was exceedingly improbable. In the lifetime of a man, things that are improbable may be treated for practical purposes as impossible. That is why you will never win the big prize on the football pools. But in our human estimates of what is improbable and what is not, we are not used to dealing in hundreds of millions of years. If you filled in pools coupons every week for a hundred million years, you would very likely win several jackpots.”Once a Replicator formed, mutations would occur and natural selection would begin—having a strong say in the way subsequent organic molecules used by living organisms would emerge and proliferate. Modern proteins, DNA and RNA were still a long way away.

More of What’s WrongThe spontaneous generation of life did not depend on the random assembly of a specific replicator, a specific molecule or any specific process. It depended on the emergence of some replicator—or an assembly of some set of simple molecules that eventually led to replication via some process that worked. In other words, calculations of probability must take into account that there are many possible pathways to life that might work—not just one that is unique. A simple example might help—

Consider a golfer playing a round of golf. He tees up his ball to play the first hole. He takes out his “driver” and hits his ball 220 yards straight down the fairway. He then walks down the fairway towards the hole and finds his ball lying in the grass. He exclaims to his friend, “Wow! Bill, will you look at that? What are the chances that my ball would land on this blade of grass? The probability must be a billion to one— that’s almost impossible.

Herein lays the fallacy behind the simplistic probability calculation carried out by Hoyle (and many others). If we could turn back the clock 4.5 billion years and start things out again, would exactly the same kind of life based upon exactly the same information-storing molecule capable of replication emerge on Earth—or would it be something different? Put another way, if we find life elsewhere in the universe—or even our own solar system—will it have the same information storage basis and replicate in the same way as ours? Not likely—many pathways are available just like there are many ‘blades of grass’ available to our golfer. What we are hinting at here is that the probability of emergence of some kind of life—given the right conditions such as exist on Earth—could indeed be 100%.

His friend, perhaps possessing a deeper understanding of statistics says, “Yes, John, but the damned ball had to end up on some blade of grass! After all—there are a billion of them out here so unless you smacked the ball into a sand trap, it’s 100% probable that it would land on one of them!”

Spontaneous Emergence of Life—Yes!A current school of thought suggests that life is an inevitable consequence of “cosmic evolution,” shaped by the fundamental laws of physics. All around us we see evidence of self-organization that has been taking place on a cosmic scale since the Universe began. Superclusters, clusters and galaxies have formed out of stars and giant clouds of gas and dust—pulled together by the action of gravity. Stars and their solar systems formed in the same way. This large scale organization of matter was driven by the energy expended during gravitational contraction.

In the case of the Sun and other stars, gravitational contraction heated them enough for nuclear fusion to start in their cores—unleashing another source of energy that now bathes all the planets in any solar systems that accompany them. This energy source ultimately drove the emergence of complexity that we now see on Earth—including life, itself.

Life—An Inevitable Consequence of Cosmic Evolution

Life is an emergent property of cosmic evolution that inevitably arises in those locations where (i) suitable materials are exposed to (ii) a suitable energy source in (iii) a suitable environment that is stable over a long period of time. The theoretician, Stuart Kauffman, has characterized life thusly—

…If all this is true, life is vastly more probable than we have supposed. Not only are we at home in the Universe, but we are far more likely to share it with unknown companions.”

“… Laws of complexity spontaneously generate much of the order of the natural world…Life is a natural property of complex systems. When the number of different molecules in a chemical soup passes a certain threshold, a self-sustaining network of reactions—an autocatalytic metabolism—will suddenly appear. Autocatalytic metabolisms arose in the primal waters spontaneously, built from a random conglomeration of whatever happened to be around. …The collective system does possess a stunning property not possessed by any of its parts. It is able to reproduce and evolve. The collective system is alive. Its parts are just chemicals.

Stepping Towards Complexity

1. Synthesis of simple organic molecular building blocks

2. Polymerization—assembly of simple building blocks into long chains.

3. Origin of the first replicator—the RNA world

4. The emergence of genetically encoded protein synthesis

5. The emergence of DNA as the vehicle of information storage

6. Last Universal Common Ancestor (LUCA)—the first cell

7. Origin of the eukaryotic cell8. Origin of multicellular life—

specialization9. The Cambrian Explosion10.Origin of humans

Cosmic Dust

Cosmic dust grains, like this one < 0.1 mm across, are found in Giant Molecular Clouds. Most are made of graphite and silicate compounds.

Ices made of H2O, CO2, CO, CH4, formaldehyde (H2CO) (which might play an role in the formation of the simple sugar, ribose), and methanol (CH3OH) form mantles around dust grains.

The icy mantles facilitate the formation of other more complex molecules. Over 130 have been identified and 65 of them are organic!

Some researchers have argued that it would have taken a billion years for complex organic molecules to form on Earth ―others say they could form in less than 100 million years. The evidence for life’s early appearance on Earth is overwhelming so either those arguing for slow formation are wrong…

or the organics formed slowly in GMC’s and then fell to Earth, like manna from heaven…and the time required for formation would be irrelevant!

Comets

Giotto images Halley’s nucleus in 1986

Organic molecules have been found in cometsSpacecraft visits to comets 1P/Halley (in 1986) and 81P/Wild 2 (in 2004) found even more complex organic compounds than have been found in interstellar space by remote sensing. They remain in frozen form in dust grains ejected from cometary nuclei as the comet approaches the inner Solar system.

Prebiotic molecules contained on these dust grains—if captured by Earth’s gravity—would float in the atmosphere for many years―ultimately falling to the surface—and the molecules would remain intact! Thus the delivery of cometary material containing prebiotic molecules that could ‘jumpstart’ the origin of life on Earth would be a virtual certainty!

Meteorites

Murchison meteorite, which fell near the town of Murchison, Australia in 1969

Over 70 different amino acids have been found in the Murchison meteorite!

Nucleotide bases, sugars and other organic compounds such as alcohols, carboxylic acids, amines and amides have also been found—in other meteorites as well!

Complex organic molecules formed in space are able to survive passage through Earth’s atmosphere as well as ground impact.

Slight excess of L over D-amino acids → processing on dust grains by circularly polarized light → explains chirality of amino acids and other biotic compounds!

Miller—Urey ExperimentSimulate primitive atmosphere H2O, CH4, NH3 and H2

Subject it to lightning

Organic molecules produced—including the sugar, ribose, and all 20 amino acids!

Early atmosphere was a secondary—CO2, N2, H2O, some CO and H2

Still obtain organics

Black SmokersWhere oceanic plates separate, hot mantle oozes up to build new crust—sea water is heated up to temperatures of 350 oC and it dissolves and exchanges minerals with the rock

Near black smokers, this heated water enriched in gasses, minerals (such as H2, H2S, CO, CO2, HCN and NH3) and ions is ejected back into surrounding cooler sea water where it interacts with catalytic clays

Sudden drop in temperature of this enriched water from 350 oC down to 2 oC facilitates chemical reactions that produce simple organic molecules and polymers—including amino acids

Chicken and Egg Paradox

Proteins can’t make more proteins without DNA and RNA, but DNA and RNA can’t be made (and its information store accessed) without proteins

…or can it?

There would be no ‘chicken and egg’ paradox if the first living organisms did not require proteins at all. Could some simple single-stranded RNA-like polymer have spontaneously formed that could catalyze its own replication without the aid of proteins? Eventually, such a structure would have evolved the ability to make proteins that would greatly accelerate the replication process. Later on DNA appeared as a more robust form of information storage, thanks to its superior chemical stability.

This idea is known as the “RNA world hypothesis.”

Which came first—the chicken or the egg?

Evidence for RNA FirstIt received support with the discovery of ribozymes, which are types of RNA that act as catalysts. RNA enzymes are ‘living fossils’, still found in today's DNA-based life. In 2001, the 3-d structure of the ribosome was deciphered—they consist of RNA and proteins—but the key catalytic sites of ribosomes were revealed to be composed of RNA. The proteins are of peripheral functional importance.

The formation of the peptide bond that binds amino acids together into proteins, is now known to be catalyzed by an adenine residue in the rRNA of the ribosome: thus, the ribosome is a ribozyme. This finding suggests that RNA molecules were most likely capable of generating the first proteins, i.e., they came first.

The existence of the ribosome supports the hypothesis that a simple RNA replicator appeared before DNA because the RNA in the ribosome contains in its structure ‘fossil’ evidence of the existence of an earlier ‘RNA world.’

The hypothesis received further support from experiments in which ribozymes were produced in the laboratory that catalyze their own synthesis—such as the RNA polymerase ribozyme.

Polymerization of RNAA dilemma—the sugar of one nucleotide must form a bond spontaneously with the phosphate of the next…and so on. However, this process of polymerization in water is not thermodynamically favored since it involves the release of water into surrounding water and thus the process will not happen spontaneously—in fact, the reaction goes the other way—polymers in water will undergo hydrolysis and break down eventually into individual monomers!

However, if there is some external energy source to drive the binding of monomers—along with the presence of some catalyst to facilitate the process—then polymerization in a water solution can occur.

Clay as a Catalyst

Polymerization in a water solution can occur when clay minerals are present in the mix. Lab experiments have shown that they catalyze the polymerization of RNA chains up to 50 nucleotides long!

Montmorillonite consists of 3 "layers"—a layer containing aluminum sandwiched between two silicate layers. They concentrate nucleotides and provide metal ions to catalyze their polymerization.

Thermodynamic Argument for the Emergence of RNA and DNA

Life is ‘an irreversible thermodynamic process’ which arises and persists to produce entropy. The production of entropy is not merely incidental to the process of life, but in fact it is the very reason for its existence. The absorption and transformation of sunlight into heat is the most important irreversible process generating entropy in the biosphere. Thus, life most probably began as a catalyst for the absorption and dissipation of sunlight on the surface of Archaean seas. The resulting heat could then be used to drive other irreversible processes such as the water cycle, hurricanes, and ocean and wind currents.

RNA and DNA are the most efficient of all known molecules for absorbing the intense UV that penetrated the early atmosphere and are remarkably rapid in transforming this light into heat in the presence of liquid water. Thus, the origin and evolution of life were inseparable from water and the water cycle and would have resulted from the natural thermodynamic imperative of increasing the entropy production of the Earth in its interaction with its solar environment.

Entropy—an Aside

The Second Law of Thermodynamics tells us which configuration came first—Nature tends from order to disorder in isolated systems—a statement that paraphrases the Second Law of Thermodynamics—or more technically—the entropy of isolated systems always increases.

Entropy and Life

An infusion of energy is needed to generate and support any system that is more complex than its surroundings—order has to be maintained.

Life is a system more complex than its surroundings. Its order needs to be maintained by a flow of energy—from a ‘hot source’ to a ‘cooler sink’.

The Sun, the Earth and surrounding space—or universe— is an isolated system—more entropy must be returned into space from the Earth than it receives from the Sun—in other words, the organization of complexity in Earth’s biosphere requires the removal of entropy.

Earth emits more long wavelength photons back into space than short wavelength photons it receives from the Sun. According to the Second Law of Thermodynamics, this process increasesthe entropy of the Universe.

The First ReplicatorSimple nucleotides could have ‘polymerized’ forming short strands of RNA in a variety of possible ways. Many combinations that formed would break apart because the strength of their bonds wasn’t very great and the energy required to break the nucleotide chain was correspondingly small. However, certain base pair sequences have catalytic properties that strengthen the bonds of a forming chain, allowing them to stay together for longer periods of time. Such chains would grow longer and attract more matching nucleotides faster until they eventually formed at a faster rate than they broke down. Thus, they would begin to proliferate on early Earth.

The emergence of such chains would mark the origin of the first primitive form of life—the beginning of an ‘RNA world’ in which different forms of RNA compete with each other for free nucleotides and are subject to natural selection. The most ‘fit’ RNA molecules—ribozymes—the ones able to efficiently catalyze their own replication—would survive and evolve, ultimately forming modern RNA.

The idea of emergence of RNA ribozymes has recently been given credence by Tracy Lincoln and Gerald Joyce of the Scripps Research Institute who ‘evolved’ two RNA ribozymes in the lab from individual RNA strands that catalyzed the reproduction of each other. The evolution of these two RNA ribozymes capable of self-replication took about an hour. Their emergence was an example of natural selection in action—it occurred as a result of molecular competition between candidate enzyme mixtures

RNA Replication Without EnzymesThermodynamic arguments hypothesize that RNA became self-replicating when the temperature of the primitive seas had cooled to somewhat below the denaturing temperature of RNA (around 70±15 °C). During the night, the surface water temperature would be below the denaturing temperature and single-stranded RNA could act as a template for the formation of double-stranded RNA. During the daylight, double-stranded RNA and DNA would absorb UV light and convert this directly to heating of the ocean surface, raising the local temperature enough to allow for denaturing of RNA (breakup into 2 single strands). The copying process would be repeated during the cool period overnight.

Such a temperature assisted mechanism of replication is similar to polymerase chain reaction (PCR), a routine laboratory procedure to multiply DNA segments.

Thus, RNA/DNA at the beginning of life did not require enzymes for self-replication—reproduction was instead promoted by the day/night fluctuation of the sea-surface skin temperature about the denaturing temperature of RNA/DNA!

Proteins Enter

Eventually, however the first replicator appeared in Earth’s primordial soup, RNA chains developed catalytic properties that help amino acids bind together. These amino acid chains were primitive proteins that assisted the synthesis of RNA, giving those RNA chains that had this catalytic property a highly selective evolutionary advantage.

The ability to catalyze one step in protein synthesis (aminoacylation) of RNA has been demonstrated in the lab in a short (five-nucleotide) segment of RNA. Furthermore, competition between various RNA chains may have favored the emergence of chains that acted cooperatively—which could have opened a pathway to the formation of the first proto-cell!

The Emergence of the CellNo other ‘mechanism of life’ has proved to be ‘more fit’ than the cell. It is virtually impossible to imagine any other mechanism that offers more advantages than those derived from the cell. For example—

Molecules synthesized within a cell’s membrane do not escape into the surrounding environment and their concentrations are maintained at desired levels by regulating their formation and break-up.

Transport of molecules thru the cell is regulated by other cellular molecules that act together in a coordinated way.

Since the molecules that are produced by the cellular machinery are based upon genetic information stored in the cell’s DNA and since these molecules interact with the cellular membrane, those cells with the most favorable interaction are the ones that tend to proliferate—in other words genes evolve based upon their products.

This physical interaction with cell membranes allows for joint maintenance of different genes within the cell’s DNA and makes possible co-evolution towards enhancing synergistic function. In essence, the cell membrane makes it possible for all cellular components to function and evolve as one well-coordinated unit. So—how did cellular life emerge?

The First CellThe current cell is the result of some three and one-half billion years of evolution. The first cell was much more primitive in its structure and make-up.

Proteins, if the RNA-first hypothesis is correct, did not exist, so the phospholipid bilayer that make up current cell membranes could not have been bio-synthesized and the protein channels that are responsible for molecular transport through cell membranes could not have existed.

The first primitive membranes were most likely fatty lipids, which spontaneously formed vesicles in water. Recent experiments have demonstrated that membranes formed out of amphiphilic-lipid chains spontaneously assemble into bi-layers and then spontaneously form vesicles. Such vesicles could have enclosed double-stranded RNA segments which then served as compartments for their replication.

Recent ExperimentsCertain membranes made of simple fatty acids, such as oleic acid, were shown to be semipermeable—small molecules like nucleotides and amino acids pass through them, but large polymers do not. Thus, vesicles that form from such fatty acids would spontaneously take in these simple monomers but would keep the larger polymers that formed inside from passing back out.

The formation of vesicles that grow—and divide—has been demonstrated in the lab.

Experimenters have incorporated short segments of single-stranded DNA into such vesicles immersed in an aqueous solution containing DNA nucleotides. The nucleotides passed through the vesicle membrane spontaneously and once inside the ‘model protocell’ lined up its matching nucleotides on the DNA template and then reacted with each other to form a complementary DNA strand. The experiment demonstrated that the first protocells that spontaneously formed contained some RNA-like polymer carrying genetic information and replicated, grew and divided without the aid of any enzymes. Proteins were not necessary.

Protocell Growth & Division(1) Membrane forms around RNA and nucleotides pass through—complementary strand forms.

(2) RNA double strand completed.

(3) Heat breaks double strand

(4) Cell incorporates more fatty acids and membrane grows.

(5) Protocell divides and daughters repeat cycle.

If protocell formed near volcanic vent—heat provided by heated water and cooling occurs when convection carries protocell into cooler water. Continued circulation would lead to cell growth until it breaks in two.

The First Cell

(1) Evolution starts with a protocell(2) RNA catalysts (ribozymes) emerge as a mutated RNA sequence. The ribozymes accelerate replication and strengthen cell membrane. Replication no longer needs an external stimulus!

(3) Metabolism begins: Other ribozymes catalyze metabolism—chains of chemical reactions that enable protocells to tap into nutrients from the environment and produce energy.

The First Cell—Continued

(4) Proteins appear: Eventually, natural selection would produce ribozymes that made proteins that could carry out a variety of tasks, such as assisting with replication and strengthening the cell membrane even more.

(5) Proteins take over: Some proteins could form bridges across the cell membrane allowing selective entry of nucleotides and nutrients needed to support chemical reactions within the cell. In addition some proteins would act as enzymes taking over the task of ribozymes.

(6) DNA appears: the enzymes would produce a more robust molecule like DNA to store genetic information and the main task of RNA would be to act as a bridge between DNA and proteins. The RNA world would be taken over by a DNA world

LUCA EmergesOrganisms resembling modern bacteria adapt to living virtually everywhere on earth and rule unopposed for billions of years, until some of them begin to evolve into more complex organisms.

Life as we know it has begun with LUCA —the Last Universal Common Ancestor.

Origin of the Eukaryotic Cell

... which during the period of 1845–1860, due to wet growing seasons, infested all of Ireland’s potato crops and led to the death of 1/3 of Ireland’s population!

Protists are unicellular and are the simplest of eukaryotes.

Some carry out photosynthesis, such as diatoms—a major group of algae.

Others move around and act like animals—such as amoebae.

… and finally some act like fungi—they act as decomposers by releasing enzymes into dead organisms that break it down — releasing materials useful to other organisms into the surrounding environment—such as water molds

Some simple protist was most likely the first eukaryote to emerge on Earth, approximately 2 Gya, which eventually gave rise to the entire line of eukaryotes

Endosymbiosis