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Biology 110 - Basic Concepts and Biodiversity

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The Origins and Diversity of Life

Terms

You should have a working knowledge of the following terms:

  • abiotic
  • monomer
  • oxidize
  • polymer
  • protobiont
  • reductive
  • replication
  • stromatolite

Introduction and Goals

This tutorial will examine how scientists think life began. This is a difficult area of scientific inquiry because it is largely speculative, however, this does not mean that any idea is valid. To be acceptable, a theory must be consistent with known chemical and physical laws. Most of the scientists who work in this area focus on how life might have arisen. By the end of this tutorial you should have a basic understanding of:

  • The origins of life's chemicals
  • The atmosphere of early Earth
  • Abiotic formation of polymers
  • The Miller-Urey experiment
  • The "primordial soup" model
  • RNA's probable role in primitive life forms

Life's History: A Perspective

A quote by J. William Schopf, UCLA paleobiologist:

"It is difficult for us to appreciate exactly how far back life has existed on Earth. One way to look at it is to imagine that all 4.5 billion years of geologic time is compressed into one 24-hour day. During the first second past midnight, earth forms. The origin of life would have occurred around 4:00 am. The oldest fossils known would have been deposited at 5:30 in the morning, just when the sun is coming up. The age of microscopic life starts then and continues all the way past noon, past 3:00, past 6:00, and in fact, it isn't until 9:00 at night that larger organisms appear. All of that evolution that you normally learn about in textbooks, from trilobites to fish to amphibians to reptiles to birds and mammals, all takes place in the last 3 hours of the day. Humans don't appear until just a scant few seconds before midnight."

Click History of earth and the solar system for a time line of major events in Earth's history. Scroll to the bottom of the screen and click on "Hadean Time" and read about how heavy elements are formed within stars.  You will be asked a question about this topic in an ANGEL quiz.

Stromatolites as Evidence For Life's Beginnings

In tutorial 14, different types of fossil evidence were mentioned. Information about early life forms has been deduced by looking at modern-day microbial communities. Some bacteria and cyanobacteria, found in certain types of marshes and lagoons, collect sediment on their sticky outer coats. These microbes migrate upward when they are clogged with sediments, thereby producing a banded pattern. This banded pattern is extremely similar to the pattern seen in stromatolites (formations of sedimentary rock with a characteristic pattern).


Figure 1. Stromatolite. Example of a layered stromatolite from the Ozarks (Precambrian era). Most often stromatolites appear as variously sized arches, spheres, or domes.

Stromatolites are thought to be the fossilized remains of ancient microbial communities that grew in layered mats and pillars.


Figure 2. A Microbial Mat. A hypersaline microbial mat from Baja California.

If we calculate Earth to be about 4 billion years old and we know that there were stromatolite-forming bacteria by 3.5 billion years ago, we must assume that living organisms arose sometime in between. Where did these living organisms come from?

Did Life Come From Outer Space?


The conditions on Earth are very different than they were 4 billion years ago. In Earth's early years the atmosphere was essentially devoid of oxygen and the planet was subjected to more lightning, UV radiation, and falling meteorites. Somehow life managed to arise under these conditions, and various hypotheses attempt to explain how this might have happened.
One hypothesis, panspermia, states that at least some organic compounds reached early Earth from space. The notion of panspermia rests on the idea that life can travel through interstellar space, driven by radiation pressure from the stars in the form of spores that occasionally come to rest on a planet where replication and evolution can occur. This sounds like great science fiction, but it is not as far fetched an idea as one might think. For example, organic compounds have been isolated from modern meteorites. However, this still doesn't explain how life itself can arise from nonliving materials. A more accepted scenario involves a type of chemical evolution in which nonliving substances became organized into organic molecules that were eventually capable of self-replication.

Chemical Evolution

As already mentioned, the atmosphere on early Earth was strikingly different from that of today. Primitive Earth's atmosphere consisted of methane, ammonia, hydrogen, water vapor, and only a negligible amount of free oxygen. This is a very important point because with a lot of free oxygen available, life probably could not have arisen from inorganic compounds. This is because oxygen tends to oxidize substances, which means that electrons are removed. Importantly, the early atmosphere was actually highly reductive (capable of gaining electrons and forming more complex molecules). Oxidation and reduction will be examined in more detail in tutorial 22.

In one proposed scenario (referred to as chemical evolution), the first organisms arose from a four-stage process. The first stage of chemical evolution likely involved the abiotic (not of biological origin) synthesis of small organic molecules (monomers) such as amino acids and nucleotides. Ultraviolet light from the sun would easily have reached the surface of Earth (ozone did not exist at that time) and would probably have been the primary source of energy to drive these synthesis reactions.

In the second stage of chemical evolution, these monomers likely joined to form polymers. Two key polymers for any type of genesis of life would have been proteins and nucleic acids.

In the third stage of chemical evolution, polymers would have aggregated into protobionts, which would have been separate entities distinguishable from their surroundings.

Finally, these protobionts would have developed some type of heredity mechanism, hence the need for nucleic acids.

Support for Chemical Evolution

Charles Darwin wrote of "some warm little pond" in which life could have begun. While this idea was initially scorned, in reality, he might not have been too far from the truth. About forty years later the Scotsman, John Haldane, and the Russian, Alexander Oparin, independently developed a model that has been called the primordial soup model for the origin of life. Basically this model suggests that complex, metabolically active molecules could arise from a slurry of simple chemicals occurring in the right proportions. This idea was tested in 1953 by Stanley Miller and Harold Urey in their classic but quite simple experiment.

In the Miller-Urey experiment, a mixture of gases (methane, ammonia, hydrogen, and water vapor) representing the primitive atmosphere was subjected to an electrical discharge. The compounds formed were then condensed and accumulated. The solution was found to contain a variety of organic compounds, including aldehydes, carboxylic acid, and amino acids. Thereby, Miller and Urey affirmed that organic compounds could arise in abiotic conditions similar to those that existed on early Earth.


Figure 3. The Miller-Urey Apparatus demonstrates the abiotic synthesis of organic molecules in a model system. (Click image to enlarge)

The Miller-Urey experiment has often been repeated, and similar set-ups have generated various organic compounds (including ATP when phosphate is added to the initial slurry). However, there are still various aspects about abiotic synthesis of organic compounds that stimulate much debate. For instance, many scientists feel that the essential ingredients for these early chemical reactions could have come from deep-sea vents (described later in this tutorial) in Earth's oceans or from submerged volcanoes, rather than from the early atmosphere.  Also, the first cells might have been autotrophs, using inorganic sulfur and iron compounds to generate their ATP, rather than consuming resources heterotrophically. Ultimately, laboratory simulations are useful for demonstrating what is theoretically possible, yet they cannot ever prove exactly how life originated on Earth. That is a matter that will likely remain open to speculation.

Clay As a Catalyst

The Miller-Urey experiments demonstrated how organic monomers could have been formed. However, these monomers were present in such dilute concentrations that it is unlikely they could have joined to form polymers. Scientists have proposed that certain types of clay might have catalyzed the polymerization of organic monomers, even in dilute amounts.

Montmorillonite is one such type of clay. It has a layered structure that can be visualized as a stack of sandwiches. In one layer there is a sheet of silica (bread), followed by a sheet of alumina (filling), and another sheet of silica (bread). Between the layers (sandwiches) are potassium ions. Ertem and Ferris (1998) performed experiments to determine which part of the montmorillonite structure actually provides the catalytic function. Via various chemical treatments, they modified the edges of the sheets and the interlayer (alumina) spaces. The modified montmorillonite was placed into solutions containing RNA monomers, and HPLC (high pressure liquid chromatography) was used to determine the length of the polymers that formed. Their results demonstrated that the edge-modified clay still produced polymers of about the same length as unmodified clay. However, when the interlayer (alumina) was modified, polymer formation was inhibited. In other words, Ertem and Ferris were able to conclude that this type of clay structure, with the alumina intact, could act as a catalytic surface in the formation of organic polymers.

Deep-Sea Vents

As mentioned, there are some scientists who think that the site of early life was deep-sea vents. These are cracks in the Earth's surface where extremely hot water, rich in minerals, is vented into very cold water deep in the ocean. (See the image on the bottom left, which shows one vent.) There are modern organisms that inhabit these places devoid of solar energy input. (See the center and right images.) Some researchers hypothesize that a reaction between iron sulfide and hydrogen sulfide could have provided the energy needed to reduce inorganic carbon to organic carbon molecules. One product of this reaction is pyrite (also known as fool's gold). Accordingly, the organic molecules once formed self-organized upon the surface of the pyrite.

Figure 4.  A hydrogen sulfide plume from a deep-sea vent (Click image to enlarge).

Figure 5.  Diversity of deep-sea vent life. This image shows some of the diversity of organisms living in deep-sea vents. The organisms include a zoarcid fish, tube worms (Riftia), and crabs. (Click image to enlarge).

Figure 6.  A cirrate octopus that lives near deep sea vents (Click image to enlarge)


An RNA World?

Once the organic polymers formed and became organized into protobionts, they needed a way to copy themselves. This is a key point in any discussion about life's origin. Most modern organisms use a DNA-based replication system, but this is believed to have been too complex for early life forms. It is generally accepted that before DNA, there was an " RNA world." However, it is not known whether RNA was the first genetic mechanism or how RNA monomers formed.

Modern RNA polymers provide much insight into the proposed function of RNA as the first hereditary unit. RNA has properties similar to DNA and proteins because it is a genetic molecule with enzymatic action. RNA is the sole genetic material for some viruses, and it serves as a carrier of genetic material in many living organisms. RNA is able to polymerize by using clay or other substrates as a catalyst. RNA can self-replicate short strands (up to 40 nucleotides if zinc is present as a catalyst).

The enzymatic properties of RNA were discovered by Cech and his co-workers in the 1980s. They found that there are RNA molecules that help catalyze the synthesis of new RNA, that remove some sequences from mRNA, and that join peptides to form proteins.

In an "RNA world," there would have been single strands of RNA with a genotype and characteristic phenotype. A single strand of RNA folds back onto itself, and portions that are complementary pair. Thus, the order of nucleotides would have provided the genotype and the 3-D folding and pairing would have provided the phenotype. This is unlike a "DNA world," where double-stranded DNA has a genotype and the proteins produced determine the phenotype. In the laboratory, some single-stranded RNA is more stable and replicates better under certain conditions. Thus, this RNA is more likely to occur in the next generation of molecules.

Combining the idea of protobionts and the "RNA world," one can imagine the early version of "mitosis." A protobiont would accumulate "membrane" molecules while the RNA inside was replicating and catalyzing the formation of short proteins. At some point the protobiont would stretch and pull, such that it split in two. Those RNA molecules that were less stable and did not replicate quickly would not be as numerous in the next generation as those that were more stable and replicated more quickly.


Figure 7.  The structure of DNA and RNA. (Click image to enlarge)

Summary

This tutorial covered some of the ideas that biologists have concerning the origin of life. Most researchers who tackle questions on the origin of life think that organic compounds first formed abiotically. The experiments of Urey and Miller demonstrated that these compounds could have formed in an atmosphere similar to that which existed on early Earth. It is also possible that organic compounds might have formed in deep-sea vents. Another hypothesis, panspermia, is that organic compounds (or perhaps life itself) arrived on the planet from extraterrestrial sources.

Once organic monomers appeared, it is hypothesized that polymers might have formed on substrates such as clay or pyrite. RNA was probably one of the first polymers to form. Polymer formation might have initially been dependent on solid substrates (like clay or pyrite), but sometime later polymer formation became independent of these solid substrates. At some point, polymers like RNA began showing signs of self-replication.

This scenario is supported by experiments that revealed that some RNA molecules have catalytic activity and that they can support the replication of other RNA molecules. Hence the beginnings of one of life's key processes, replication. In one proposed scenario, an early progenitor of a cell, a protobiont, might have cooperated with RNA molecules to form a structure that more efficiently favored the replication of RNA. Molecules of RNA enclosed in such an early protobiont would have more efficient replication of those molecules that were floating free, thus they would show preferential reproduction. It is interesting to speculate whether or not this constitutes a primitive form of natural selection; if so, then perhaps a protobiont with self-replicating RNA really does represent a primitive form of life.

Added by Anonymous , last edited by RICHARD CYR on Mar 29, 2010 11:16