25. Early Earth and Life Processes

Transcript: The tree of life suggests that the first organisms on Earth were thermophiles, organisms that accustomed to and thrived in conditions of high temperature. The environments may have been hot springs or deep sea ocean vents. They came from two of the three branches of the tree of life, bacteria and archaea. They were prokaryotes or cells without nuclei. It’s possible that eukaryotic organisms also coexisted with the prokaryotes. They would not have left fossils, and we may not know when eukaryotes first evolved. The first organisms gained their energy from chemical reactions with hydrogen, sulfur, and iron compounds. These chemistry elements were abundant in the early Earth. They also evolved rapidly. The DNA had many copying errors. So there was rapid experimentation, and the natural selection operating on these different forms of chemistry would have proceeded very effectively.

Transcript: In general, evolution proceeds from simple to more complex forms of life, but it’s not the unique and defining attribute of evolution. Simple organisms can be extremely well adapted. Anaerobic bacteria have survived on this planet for over three billion years. No large and complex creature has ever lived for more than a few tens of millions of years. Also, early life was not that much less complex than current large life forms. We share forty percent of our DNA with simple yeast. In the early history of the Earth, the complexity of DNA and the diversity of chemical reactions rose relatively quickly in the first few hundred million years of life, and it has not increased in complexity dramatically since then.

Transcript: The existence and abundance of extremophiles on Earth has implications for the search for extraterrestrial life. Remember that the entire idea of a habitable zone is predicated on a range of distance from a star where water can be in a liquid form. Perhaps this is too limiting an assumption. The first organisms on Earth were extremophiles, so maybe extremophiles formed first elsewhere in the universe and are relatively abundant. The wide range of physical conditions for extremophiles on Earth implies a wide range of possible environments for life. Perhaps life does not just form on a temperate watery planet but in more extreme conditions on other types of planets or Moons.

Transcript: Certain life forms can exist under extreme chemical conditions. Examples include halophiles that prefer a high salt concentration, above five percent all the way up to thirty percent. For comparison, seawater has a salt concentration of three percent, and it’s toxic to humans. Environments where halophiles exist might be a great salt lake or other salty environments, either on land or in the ocean. Other examples of important organisms on Earth that have extreme chemical conditions are anaerobes or oxygen hating organisms. These often use sulfur dioxide or carbon dioxide for their respiration. Examples include mammals intestinal tracts, ocean sediments, and hydrothermal vents deep on the ocean floor.

Transcript: Life forms on Earth can exist and thrive in extreme chemical conditions corresponding to acid or base. Acidophiles can thrive in conditions where the pH is less than five. That's similar to sulfuric acid. Examples include the sulfur pots in Yellowstone Park, volcanic soils, and of course the gastric fluid in the human stomach. At the opposite extreme are alkaliphiles which can exist and thrive at pHs greater than nine. Examples include soda lakes in Africa and soils that are rich in carbonates.

Transcript: There is a set of organisms that can persist and thrive under conditions of extreme pressures. They are called barophiles. Barophiles can exist at pressures of hundreds of atmospheres. These environments are typically found in the deep sea. For example, there are entire colonies of eukaryotes on the continental shelf. Sea cucumbers and other creatures also exist under very high pressure, and there are microorganisms that thrive near deep sea black smokers. At the other extreme many organisms can do well at conditions of low pressure or high altitude on the Earth’s surface. At the top of the highest mountains there are algae, plants, even insects, and in laboratory experiments certain insects have survived at pressures less than one-tenth of the pressure at sea level.

Transcript: In the 1970s, scientists who used the first deep sea submersibles to go thousands of feet below the ocean’s surface got a huge surprise. They found entire ecosystems near deep sea ocean vents where hot superheated water existed due to volcanic activity on the ocean floor. This is a region of utter darkness. Light can of course only penetrate the first few feet under the ocean. It’s also a situation of extreme pressure, perhaps a hundred atmospheres, and yet in this extreme pressure and at a temperature of superheated water, six or seven hundred degrees Fahrenheit, organisms were found. The organisms gained their energy by metabolizing hydrogen sulfide, a toxic chemical to us, from the deep sea vents. In addition to the microbes were larger organisms. In a sphere extending out from the microbes at the hottest temperature were other larger organisms feeding on the microbes. Beyond that, transparent krill eating the smaller organisms, and beyond that, substantial sized fish who did not have eyes, there was no light for them to see, but moved by sonar or infrared vision. This was a huge surprise, the existence of entire ecosystems hidden from us on the ocean floor. In addition, these are ecosystems that live independent of sunlight. Their energy comes from the core of the Earth.

Transcript: Many microbial organisms on Earth can survive extremes of temperature. Thermophiles is the name for organisms that like heat. Thermophiles have been found that can exist in the temperature range forty-two to a hundred and thirteen degrees centigrade. That's a hundred and seven to two hundred and thirty-six degrees Fahrenheit, well above the boiling point of water. Examples of these organisms are found near deep sea geothermal vents and in Yellowstone National Park. At the opposite extreme are psycrophiles, creatures or organisms that like extreme cold. Psycrophiles have been found in the temperature range down to minus three degrees centigrade up to twenty degrees centigrade. That is creatures that like to live below the freezing point of water. These have been found in snow fields in Antarctica, on the surface of glaciers, and in the deep sea ocean far from vents where the temperature is very cold.

Transcript: We tend to think of the evolution of life in terms of a sequence from simple organisms to large and complex organisms, but we should remember that even now, most life on Earth looks nothing like us. There are many more prokaryotic species, involving cells without nuclei, then eukaryotic species. There are many more species that can survive physical conditions that would kill us then there are large and complex organisms like us. Collectively, these species are called extremophiles. They like and thrive on extreme physical conditions. They are drawn from two of the three main branches of the tree of life, bacteria and archaea. Extreme life forms are common on this planet, and extreme conditions have been common in the history of this planet so naming them extremophiles is just a matter of definition.

Transcript: If you looked at a biology book from a hundred years ago or even fifty years ago, you would have seen a diagram called the tree of life. In the traditional version of this diagram, it is represented as a tree. The simplest organisms are at the bottom of the tree, and more complex, sophisticated, or intelligent organisms are higher up the tree. In traditional representations of the tree of life, primates and humans are at the pinnacle of the tree or the apex representing the highest form of evolution. The tree of life is seductive because it gives the sense that all evolution was leading up to this point, to us at the pinnacle of creation and evolution after billions of years. The traditional tree of life has now been replaced by modern biology’s version of the tree of life based on deviations of DNA and the idea of a common ancestor in DNA for every living form on the Earth. The modern tree of life has many branches and pieces, but basically it’s simple. There is a common ancestor and three major branches on the tree: one corresponding to bacteria, one called archaea, and the other for eukarea. In the branch for eukarea, plants, animals, and fungi form three twigs on the branch, and humans are of course a tiny twig off the animal twig. This means that contrary to the traditional view, humans are just a twig on the tree of life and not the center of creation or the endpoint of evolution.

Transcript: The modern version of the tree of life based on the sequence of DNA can be used to speculate about the earliest organisms on the Earth. It’s important to realize that the tree of life is only tracing genetic differences in the DNA sequence, so it’s not possible to put an exact time sequence on these changes. Evolution occurred at different rates at different periods of the Earth’s history. For example, the mutation rate early on was much higher than it is now. It’s likely that the three major branches of the tree of life, bacteria, archaea, and eukarea, split off relatively early three and a half billion years ago. It’s also likely that the original organisms, those closest to being the last common ancestor, were quite different from modern day organisms. They were extremophiles, organisms that thrived in unusual and extreme physical conditions.

Transcript: Similarity or dissimilarity in DNA can be used to trace human origins. The oldest human civilizations date back only ten thousand years, the oldest human artifacts about thirty or forty thousand years. Yet changes in the structure of DNA can be used to trace human origins back hundreds of thousands of years, even millions of years. The first human ancestor dates back to two or three million years ago. By watching the change in DNA as artifacts are found in different parts of the planet, it’s possible to show how human pre-ancestors moved across our planet. The earliest humans lived in Africa. They subsequently migrated to Europe and Asia and then across the land bridge to North and South America. These genetic differences are traced in present day humans. For example, this activity called forming phylogenetic trees can be used to show that racial differences, the superficial differences between people of African, or Asian, or European descent, are utterly trivial when considered in terms of DNA. The typical variation in the DNA between two people, any two people, from one race is as large as the typical differences in DNA between the races. Thus, the races and their differences are truly superficial. At the level of DNA we are all the same.

Transcript: Fossils have existed only since creatures had skeletons or hard bodies or shells, about a half a billion years, but life existed on Earth at least three billion years before that. Almost all of these life forms were microscopic. Scientists can learn about the history of microscopic life over the whole span of Earth’s history from DNA itself, which acts as a kind of living fossil telling the story of life. Imagine the DNA of an early living organism that was the ancestor of all life today. Over time, genetic changes would accumulate and the accumulated changes cause species to diverge in an evolutionary sense. So now looking backwards, we can estimate the time to a last common ancestor by the cumulative amount of changes to the DNA. Two species with more similar DNA must have diverged more recently in the evolutionary tree. Not all the changes are due to mutations. Sometimes entire genes can be incorporated, a process called lateral gene transfer.

Transcript: Natural selection operates at the level of species interacting with their environment. At the microscopic level, DNA copies itself, a mechanism that is generally extremely efficient and effective, but its not perfect. The human cell copies the entire information in the human genome, three billion bases, in only a few hours. The error rate is tiny, one in a billion. However errors do occur, errors in transcription, alterations caused by ultraviolet radiation, and even the effects of dangerous chemicals that we call carcinogens. All these lead to mutations or changes in the DNA that are then propagated to successive generations. Some mutations are utterly harmless. Others can be fatal to the organism, for example, when they prevent a vital protein from being created. However some mutations will be beneficial, and when those are passed on, through the operation of natural selection we see that mutation is an essential part of the biological process.

Transcript: The earliest solid evidence for life on Earth comes from three and a half billion years ago in the form of stromatolytes. Stromatolytes are prokaryotic organisms, colonies of microbes, bacterial mats. They take the physical form of layers of sediment interspersed with microbes. Today they are found in their fossilized form, but the layered structure is very clear evidence of a colony of organisms. The energy source for the prokaryotes was photosynthesis near the top of the bacterial mat. Organisms lower down existed on the waste products of organisms that were receiving direct sunlight. Even today, we can see the descendants of stromatolytes. In Western Australia for example, it’s possible to see bacterial mats even today that exist and get their energy in a similar way to three and a half billion years ago.

Transcript: The first biological systems capable of independent life on Earth were prokaryotes. Bacteria are familiar example, a single long strand of DNA with several thousand genes. Most prokaryotes are harmless to humans, and in fact they are essential for our form of life and for the survival of more complex organisms. Prokaryotes may have less genetic material than eukaryotes, but they are highly complex chemical factories, many of which are still not understood. In fact, the diversity of chemistry of prokaryotes is still only imperfectly measured because its very hard to culture these in the lab, but in a single teaspoon of seawater there is more genetic material in prokaryotes then in the entire human genome.

Transcript: There are two fundamentally different types of cells in life on Earth: prokaryotes and eukaryotes. The prokaryotes are cells without nuclei. They are ten times smaller then the eukaryotes, and they are far less complex in a chemical sense. Eukaryotes, which are larger, have their DNA contained in a nucleus which provides a higher level of functioning and complexity. Examples of prokaryotes are E coli and salmonella. Examples of eukaryotes are amoeba and of course the trillions and trillions of cells in our own bodies. Prokaryotes evolved first and lead to eukaryotes, but both are essential for life on Earth. Although we are more familiar with material that includes cells with nuclei, there are more examples of prokaryotic organisms on Earth than there are eukaryotes, and the small organisms like bacteria are essential to the functioning of the higher level organisms. The reverse is not true. Prokaryotes could exist quite happily without the existence of cells with nuclei.

Transcript: The history of life on Earth is a story of experimentation; initially, the experimentation of chemical reactions, then the experimentation of biological processes, and finally that of genetic variation itself. These genetic variations and earlier variations are molded to the environment, which ensures the survival of the fittest organisms; this is the basis of natural selection. At a chemical and biochemical level, life has formed specific and efficient solutions to its problems, usually for energy efficiency reasons. Life uses only 20 of the 92 elements in the periodic table for its essential processes. It uses 20 out of 100,000 possible amino acids. It uses 10,000 out of a nearly infinite number of possible proteins. Many complex molecules have two-handedness, or mirror images of themselves. Early on in the history of life, life selected one of the two-handedness; for example, all the amino acids in life on Earth use the left-handed molecule, not the right-handed molecule. This, incidentally, is the reason we do not believe life originated from space, because in meteorites equal numbers of left- and right-handed molecules are observed.

Transcript: Cells are tiny chemical factories, and they are essential for every complex life form on Earth. They have several major ingredients that are important for their function. Carbohydrates are the basis of all the structures in cells. In the every day world, we are familiar with carbohydrates because they can store energy. Other carbohydrates involve cotton, wood, cellulose for example. Lipids are important because they store energy, and they were used to form the first barrier and therefore cell walls, and finally proteins, which are the workhorses of cells, engaging in a wide array of chemical reactions. The particular form of proteins called enzymes are essential in cell function because they participate in reactions but are unchanged by them. These forms of proteins act to accelerate reactions and can be used many times, making the efficiency of the chemical work of a cell very high.

Transcript: A major step in the development of life is the transition from free floating organic molecules in water to cells. Biology cannot develop without some form of compartment or membrane to concentrate chemical reactions and protect the entity from the environment. Scientists do not yet know how this transition occurred on the early Earth, but it’s been shown that the heating and cooling of solutions of amino acids can lead to the formation of a cell-like structure called a proteinoid. Proteinoids are not alive, but they can grow by allowing amino acids to pass through the membrane and eventually they will split. They also can store energy, in some cases, by storing a voltage across their surfaces. So proteinoids and other similar entities may have been the precursors to cells. It’s likely that on the early Earth, this transition occurred steadily and slowly. The selective advantage of cells was probably not obvious for awhile, and so there is no particular time when we can say the first cell developed.

Transcript: The construction of larger organic molecules from smaller pieces, even if there’s a mechanism for it to operate, is essentially a random process and not directed in any way. So how did this process continue to build larger and larger chain molecules? RNA strands can catalyze their own creation, and this leads to a microscopic version of natural selection. The RNA strands that replicated faster and more efficiently and with fewer copying errors were able to dominate the biochemical soup. So RNA adapts to its environment and grows because those successful strands at copying and building will survive and dominate in the population. DNA is more versatile and less prone to copying errors then RNA, so the natural transition from RNA to DNA, which may have taken a hundred million years or more, is also a logical progression based on the same principle.

Transcript: If RNA was the first replicating molecule on Earth, how was it built? Fred Hoyle, a theorist in astronomy, speculated that it was incredibly unlikely to build long complex chain molecules from small pieces by chance. He said that it was as unlikely as if a whirlwind passed through a junk yard and fully assembled a jumbo jet. Turns out he was wrong because both in theory in computer simulations and in the lab simple autocatalytic networks of chemicals can rapidly build complexity, but a mechanism is needed to build long chain molecules. Biologists speculate that clay or perhaps iron pyrite on the early Earth provided the template for building long molecules. Clay is a silicate that’s reacted with water. Molecules from the organic soup could cling to the clay and the repetitious structure of the atoms in the clay was aiding the assembly of long chains. Hundred base pair sequences have been produced this way in the lab, and it’s possible that given sufficient time, long chains could be created this way. Thus, the idea of an RNA world is not so far fetched.

Transcript: DNA was probably too complex to have been the first replicating molecule in the history of life. RNA is much simpler. It has only one strand, and it would be easier to construct from smaller pieces. However, neither molecule can reproduce itself without enzymes. Enzymes are proteins that take their instructions from the DNA itself which leads to a classic chicken and egg problem. This problem was solved in the 1980s by Thomas Cech who showed that RNA can catalyze biochemical reactions in the same way that enzymes do leading to the probability that RNA could facilitate its own replication. Thus, the early Earth may have been an RNA world where RNA was replicating and facilitating its own reactions. In the totality of biochemistry, there are other possible replicating molecules, and perhaps life elsewhere in the universe has used these.

Transcript: In addition to being built up from smaller pieces by natural chemical reactions, organic molecules were brought to Earth by impacts early in the Earth’s history. Meteors have been shown to contain amino acids, a significant number of them, and other complex molecules. Complex molecules and organic material therefore can form and survive in deep space and can probably survive in the interior of an impacting object when it lands on the Earth. Thus, especially early in the Earth’s history, asteroids, comets, and meteors must have deposited a lot of organic material on the Earth’s surface. An extension of this idea which is a little more radical, is called directed panspermia, the idea that complex organic materials came to the Earth from far beyond the solar system as the Earth and the Sun and all the planets travel through interstellar material. There is no direct evidence that life origins come from beyond the solar system. However we have the case of Martian meteorites which can travel to us from Mars. Material traveling around the inner solar system could have transcribed and brought early organic material. In a sense, we might all be Martians if Martian meteorites with early life forms had seeded life on Earth. Nobody knows if this is a likely scenario yet.

Transcript: How did life begin on Earth? In the 1950s, a classic set of experiments were conducted by Miller and Urey. The Miller-Urey experiments tried to make life in a bottle. A flask containing water and the basic chemical ingredients of the oceans and the Earth’s atmosphere is given extra energy and left for weeks. After watching this closed experiment for weeks, it turns out that amino acids and complex molecules and other organic material is created. The Miller-Urey experiments give some sense that complexity can emerge from simple ingredients given sufficient time and an energy source. However, in the 1950s we did not know exactly what the early Earth’s atmosphere composition was. It turns out that the first Miller-Urey experiments used too much methane and ammonia and not enough carbon dioxide. Using a more appropriate composition for the early Earth’s atmosphere yields less organic materials, but later versions of these experiments have nonetheless been able to reproduce and produce almost all the amino acids, sugars, lipids, and the five bases needed by RNA and DNA. This is of course not the same as producing a replicating molecule, which has never been seen in one of these experiments, and in fact other chemical constituents are probably needed in addition to a large amount of time to produce the first replicating molecule. But it is an indication that life must have started by the building of larger pieces from smaller pieces.

Transcript: The early Earth was a geologically active place. Not long after the crust had cooled, there was a large amount of tectonic activity. The core of the Earth was cooling, and heat was radiating outwards driving geological activity. The early active Earth indicates that one of the most likely places where life may have started is in the deep sea because ocean vents opening up from the magma below will have heated the water and could have supported life. Ironically, the land masses or shallow ponds are the least likely places for life to have started because of the damaging effects of ultraviolet radiation. There is strong genetic evidence that the earliest ancestors of ours in the microbial form were heat loving organisms that began deep in the ocean.

Transcript: The principle constituents of the early Earth’s atmosphere were nitrogen, carbon dioxide, and water vapor. There was essentially no oxygen because oxygen has been produced by microbial organisms over the succeeding billions of years. Because there was almost no oxygen, there was also no ozone. Ozone acts as a protective shield in the upper atmosphere on the current Earth to protect life forms and organisms from damaging ultraviolet radiation which would otherwise cause cellular damage and alter the DNA itself. The fact that the early Earth had no oxygen or ozone means that it’s very unlikely that life got its start on the land masses of the early Earth because of the damaging effects of the radiation.

Transcript: When James Watson, co-discoverer of the structure of DNA, was asked by a journalist the importance of his discovery, he gave an interesting answer. “Life is digital information.” We can follow this analogy in looking at the different structures of life. The simplest unit of information is a base, one bit, maybe like a letter in the English language. A base has ten atoms and joins strands of DNA. The next unit up is a codon, corresponding maybe to a word in the English language. A codon has six bits of information and is composed of about a hundred atoms and controls the genetic code. Next unit up is a gene, like a sentence in the English language, with a hundred to a thousand bits of information, a thousand to a hundred thousand atoms. A gene determines a characteristic of an organism. Next we might consider a bacterium or a simple life form. It’s like a short book in the English language, has maybe a hundred thousand to a million bits and a million to ten million atoms. Finally, the human organism, a complex organism, information content equivalent to an encyclopedia, six gigabytes, and thirty billion atoms in the complete genetic information of a human being.

Transcript: The sequence of base pairs along the long DNA chain molecule is the genetic code. Think of it as a four letter alphabet, A,T,G, and C, combining according to particular rules and many base pairs in sequence. The basic piece of information in the genetic code is called a codon, a triplet of base pairs. With four possibilities for each, a triplet can code four cubed or sixty-four amino acids. Since there are only twenty amino acids used by life, there is a fair amount of redundancy in the genetic code which allows for transcription errors. A gene, the basic unit of information that describes a characteristic of an organism, corresponds to one hundred to five hundred amino acids making up a protein. An entire organism like the human being is composed of order a hundred thousand genes. That's the human genome, the total of thirty billion base pairs.

Transcript: The blueprint of life on Earth is DNA and its close relative RNA. DNA, deoxyribonucleic acid, is a long polymer in the form of a double helix. Its structure was first worked out by James Watson and Frances Crick in 1953. DNA has two long strands and rungs connecting the strands. Each rung is a series of base pairs. There are four bases; adenine, cytosine, guanine, and thymine, A, C, G, T abbreviated, that form the sequence of base pairs. The rules for the connection of the two sides of the ladder are that A can only connect to T and G can only connect to C, and in this way when DNA splits and recombines, the information is transcribed. This is the basis of the genetic code.