Origin of Life

The first chapter of Genesis contains the Christian account of the origin of life. It tells of God creating the heaven and the Earth, plants and animals, and then man in God’s image. All in six days. The Bible doesn’t state when this creation occurred, but most early Christians probably assumed that this did not occur too long ago. In the 1600’s, the Anglican bishop James Ussher fixed the date of creation at 4004 B.C.E. This is the established biblical view that continues to the present.

Physicists tell us, however, that the universe began between 10 and 20 billion years ago, at a moment in time they call the Big Bang. As soon as there were rocks to record the existence of life, we find evidence that life is there. How did this diversity of life appeared on Earth in a very short time span (from a geological point of view)? This is the materialist view that I try to explain in this series of articles on the origin of life.

• In the Beginning: The early planet Earth was a really miserable place. The way that the planet was formed, with ever larger and larger chunks of material slamming into it, created an enormous amount of heat. When the planet first formed it was melted. It was no place where one could ever conceive the origin of life. Less than a billion years later, however, the fossil record clearly shows that life was there.

• Miller’s Experiment: In 1953, Stanley Miller conducted his famous (or infamous) experiment. For decades, scientists had speculated whether the complex organic compounds characteristic of living things could have somehow been generated spontaneously on the early Earth. Spontaneous generation of organic compounds can’t happen today. This is because organic compounds are too fragile.

• Polymerization: The significance of Miller’s experiment was simply to show that non-biological processes could result in the formation of organic molecules, including amino-acids and nucleotides. These molecules that Miller got, however, were still relatively simple. They thus only represented a first small step.

• Primitive Cells: We know that the organic molecules that make us up are not just a jumble of things floating around in a primordial soup, they are highly ordered. They come in highly ordered packages. There are many such packages in living systems, but the most fundamental one is what we call the cell. All living things are made of units called cells. Minimally, for something to be living, requires a barrier between the living part and the non-living part. That barrier is what would define the cell.

• The Genetic Code: How does a living system reproduce? What minimally do we need to get reproduction? How reproduction arose is an especially tricky problem. It is the problem that is most debated today in the area of the origin of life.

What is Life, Part III

Even armed with NASA’s pragmatic definition of life, it is almost impossible to know what Earth’s very first life form was like. One very real possibility is that planet Earth’s earliest life may have been vastly different from anything we know today. Many experts suspect that the first living entity was not a single isolated cell, because even the simplest modern cells incorporate bewildering chemical complexity.

Most researchers assume that the first life form did not use DNA, given its exceedingly intricate mechanism. It may not even use proteins, which today act as the chemical work horses of cellular life. Naturally, experts propose different ideas regarding Earth’s first life form. Geologists propose that the Earth’s earliest living entity which fits NASA’s definition was an extremely thin molecular coding on a rock. It is easy to imagine the simple behavior of such flat life. It would have just spread across minerals in a layer of only a few billionths of a meter thick. Flat life would have exploited energy-rich mineral surfaces, and slowly spread outwards, from rock to rock.

Whatever that life form looked like, it must have arisen from chemical reactions among the oceans, the atmosphere and rocks.

Our Tendency to Dichotomize

The French anthropologist Claude Lévi-Strauss investigated the mythologies of many cultures. In the process, he recognized deep human tendency to reduce all sorts of complex situations to oversimplified dichotomies. We tend to divide people into friend and enemy. We divide the afterlife into heaven and hell. We divide actions into good and evil. We all know that most situations are much more subtle and complex.

The long history of sciences reveals that scientists are in no way immune to the trap of this kind of oversimplification. In the 18th century, for example, one group of naturalists called the “neptunists”, favored a watery origin for rocks. They fought many battles with the “plutonitsts”, who favored heat to describe the origin of rocks. It turns out that both were right. Rock sometimes form by the action of water, and sometimes by the action of heat, and sometimes even by a combination of both.

A similar contentious and misleading dichotomy raged between 18th century geologists was the one between catastrofists and uniformitarians. Catastrofists espoused the view that brief and cataclysmic events like earthquakes and floods dominated the geological history of Earth. Uniformitarians countered that geological processes are for the most part gradual and ongoing. Again, both groups were correct. Geological changes occur gradually over millions of years, but discrete catastrophic events, like the impact of big asteroids, also influence Earth’s history.

Similarly, there was a time when sharp distinctions were seen between plants and animals, and between single celled and multicellular organisms. Now, those sharp distinctions have become blurred.

I believe that any attempt to formulate an absolute definition of life, one that tries to differentiate between “life” and “non-life”, must represent a similar false dichotomy. Here’s why. It is obvious that the first living cell did not just appear fully formed with all its chemical complexity and genetic machinery. Rather, life must have arisen through a stepwise sequence of emergent events. I see life’s origin as a process of increasing chemical complexity.

What now looks to us as a divide between non-living matter and living cells tends to obscure the fact that the chemical evolution of life occurred in a stepwise sequence. Most of that history is lost, because when modern cells emerged, they quickly consumed all traces of the earlier stages of chemical evolution. They ate the evidence.

Our challenge is to use every available clue to establish a progressive hierarchy of emergent steps, leading from a prebiotic Earth rich in organic molecules to clusters of molecules, to self-replicating molecular systems, to encapsulation and membranes, to cellular life.

This view of life as a stepwise sequence of emergent events also informs the central question “what is life”. Any attempt to define the exact point in which a system of gradually increasing complexity becomes alive is intrinsically arbitrary. Where you or anyone tries to draw such a line is a question more of perceived value than of science. For example, if you value the intrinsic isolation of each living thing, then, for you, life’s origin probably would correspond to the stage when encapsulated cell membranes appeared. Perhaps you most value life’s ability to reproduce. If so, self-replication would be the demarcation point for life.

Many scientists today place special value on information as the key to life. They argue that life began with a genetic mechanism to pass information from one generation to the next. In this context, the question “what is life” becomes fundamentally a semantic question. It’s a subjective matter of taxonomy, rather than any absolute divide. Nature supports a rich variety of complex emergent chemical systems. Scientists are learning to craft a wide variety of those systems in the laboratory as well, but no matter how curious or noble the behavior of these systems may be, none of them comes with a label “life” or “non-life”.

Don’t get me wrong, labels are extremely important. They are vital for effective communication. However, I think that defining life is not helpful because there is so much we don’t know. Early attempts to classify animals purely by their color or shape ultimately failed. Similarly, early efforts to classify chemical elements according to their physical state (solid, liquid or gas) were unhelpful in elaborating a chemical theory.

We are in no position to define life. We don’t know if life’s biochemistry is highly constrained, or if there are many chemical solutions to life. It is much better at this point to keep an open mind and just describe the chemical characteristics of whatever we find.

What is Life, Part II

So, here we continue with the “what is life” issue. A general definition that’s able to distinguish all imaginable living objects from the diversity of non-living objects remains elusive. Even today, we know relatively little about the cellular life on Earth. It’s been said that a shovel full of soil would contain hundreds of microbial species that are unknown to science. That’s not to mention the vast range of plausible non-cellular life forms that might be discovered elsewhere in the universe.

I have to conclude that endorsing any sweeping definition of life based on so little knowledge is like trying to define music after listening to a single Elvis Presley song.

Top-Down and Bottom-Up

So, what do we do? As you can imagine, scientists crave a definition of life. Such a definition remains elusive, but they adopted two complimentary approaches in their efforts to distinguish that which is alive from that which is not. On the one hand, many scientists have adopted the top-down approach. Top-down refers to the effort to scrutinize all modern living organisms and fossil entities to identify the most primitive forms that are or were alive. It turns out that primitive microbes and ancient fossils have the potential to provide relevant clues about life’s early chemistry.

I must say that I find this top-down strategy inherently limited. At least so far, all known life forms are based on biochemical sophisticated cells containing complex molecules, including DNA and proteins. Any definition of life based on top-down research is limited to what appears to be modern biochemistry.

By contrast, a small but determinate army of investigators adopt the so-called bottom-up approach. The principal objective of bottom-up researchers is to device laboratory experiments to mimic the emergent chemical process of environments in the ancient Earth. Ultimately, the bottom-up goal is to synthesize a self-reproducing chemical system in the laboratory. That’s an effort that might help clarify the ancient transition from non-life to life.

You might think that all bottom-up researchers hold a common view of what would constitute the first synthetic life form, but research actually leads to an amusing range of diverging opinions regarding what’s alive. Each scientist has a tendency to define life primarily in terms of his or her own chosen chemical or biological specialty. One notable group focuses on the origin of cell membranes. To them, life began when the first encapsulating membrane appeared.

Other well respected research teams study the emergence of metabolic cycles. Those are the process by which cells gather and use atoms and energy. Naturally, for them, the origin of life coincided with the origin of metabolism. Lots of other groups investigate the origin of primordial RNA, which many experts consider to be the first genetic material. For them, the origin of RNA is equivalent to the origin of life.

There are many other workers who focus on viruses, minerals or even artificial intelligence; and each researcher advocates his own definition of what constitutes life.

NASA’a Definition

Into this mix, quite a few philosophers, theologians and science fiction writers have injected a variety of more abstract views and speculations on the possible phenomena that might said to be alive. The possibilities seem endless: counscious clouds in space, high temperature silicate minerals, a self aware internet. Such proposals sound at times farfetched, but there is so much we don’t know.

Consequently, the scientific community, with the support of NASA and other governmental agencies, holds regular meetings to explore the definition of life. After all, if one of NASA’s primary missions is to look for life on other worlds, then we’d better have a clear definition for planning future missions. It’s amazing how the “what is life” question sparks passionate arguments.

Gerald Joyce, a biologist working at the Scripps Research Institute, developed a widely accepted definition for life, at least in the context of NASA’s space exploration. He concluded that “life is a self-sustained chemical system capable of undergoing Darwinian evolution”.

According to this opinion, life incorporates three distinctive characteristics. First, all life forms must be chemical systems. That means that computer programs or robots are not alive. The second characteristic is that life grows and sustains itself by gathering energy and atoms from its surroundings. That’s the essence of metabolism. Finally, all living entities must display some sort of variation. According to the concepts of Darwinian evolution, natural selection of more fit individuals inevitably leads to evolution and the emergence of more complex entities. A system that does not have the potential to evolve does not fit this definition of life.

There’s still so much we don’t know, but this NASA inspired definition is probably as general, useful and concise as anyone is likely to come up with, at least until we discover more about what’s actually out there.

What is Life

We usually think that life is easy to recognize, that it would be obvious if something is alive or not. It turns out that is not that easy. The question “what is life” is asked in very different contexts by different groups of people. For centuries, theologians have hotly debated life’s definition and relation to the beginning of human life. Does life start at the moment of conception? Or does it begin when the brain’s first response, or with the heart’s first beat? In some theological doctrines, life commences not with a physical process, but rather at the unknowable supposed instant known as “ensoulment”.

At the other end of our human journey, doctors, lawyers and politicians require a definition of life in order to deal ethically with patients with brain death. As we saw with the contentious case of Terri Schiavo (the woman who spent more than a decade in comma), lots of people have intense and emotional views on this issue.

In sharp contrast with these ethically difficult and emotionally charged issues, are the more abstract ongoing scientific efforts to define life. A must read book on the origin of life is Noam Lahav’s “Biogenesis”, which was published in 1999. Lahav’s works in the Hebrew University at Jerusalem, and he has been involved in origins research for almost 40 years. His book is filled with insights, as well as countless technical details. As part of his text, he prepared an appendix with lots of different scientific definitions of life, which are written by over 48 different authorities.

These definitions span 150 years period, from the mid 18th century to the late 20th century. It’s worthwhile thinking about a few of those:

- Alexander Oparin: he reflects the view of many authorities. Life can be defined by a combination of traits. He says: “Life may be recognized only in bodies which have particularly special characteristics. These characteristics are peculiar to living things, and are not seen in the world of the dead.” What are these characteristics? In the first place, there is a definite structure or organization. Then there is the ability of organisms to metabolize, reproduce others like themselves and the response to stimulation. The problem is that Oparin’s characteristics are not unique to life. Many non-living systems have definite structure and organization (think about your car or your PC). Oparin says that organisms obtain energy from their surroundings to grow and reproduce, but fire does that also. Many natural non-living systems, such as flowing water or drifting clouds, respond to stimulation.

- John Desmond Bernal: an influential 20th century biological theorist, who provides a longer list of characteristics. He says: “Life is a partial, continuous, progressive, multi-form, and conditionally interactive self-realization of the potentialities of atomic electron states”. I don’t know about you, but that definition seems to be hopelessly fussy and unhelpful in distinguishing life from non-life.

- Stuart Kauffman offered a more promising definition of life in 1993. He claimed: “Life is an expected collectively self-organized property of catalytic polymers”. Embedded in this statement are a couple of key ideas. Kauffman said that life is self-organized. That is, life is a collective emergent phenomenon. He also states that life relies on chemicals to promote the production of more copies of themselves. In Kauffman’s view, life might be a relatively simple collection of self-replicating chemicals. That includes much more primitive entities than modern cellular life.

- John Maynard Smith proposed a short and persuasive definition of life in 1975. He describes life as “any population of entities which have the properties of multiplication, heredity and variation”. Here Smith introduces two key ideas and thus comes closer to a useful set of criteria. First, all life possesses information that’s passed from one generation to the next. That key idea of heredity may not be unique to life, but it is certainly one of life’s most important characteristics. Second, life displays variations. In life, heredity isn’t perfect like a Xerox copy. Variation, in turn, leads to evolution by natural selection.

Lahav goes on and on citing definitions of life, and remarkably, no two definitions are the same. I think you can see this lack of agreement might represent a problem for those of us who search for signs of living organisms in other worlds, as well as for anyone interested in the origin of life. After all, how can you be sure that you discovered life, or that you figured out the process of life origin, when you can’t come close to defining what exactly life is? In spite of generations of work by hundreds of thousands of biologists, we still have no universally accepted definition.

To be continued…

A History Of Life, Part IV

The evolution of eukaryotic cells is thought to have occurred 1.5 billion years ago or so. This led to an enormous diversification and innovation. The pace of evolutionary change quickened. Eukaryotic cells diversified into a broad range of single-celled organisms. Most strikingly, some lineages of eukaryotic cells gave rise to true multicellular organisms. The evidence for when multicellular organisms first appeared is conflicting. If we look at the molecular phylogenetic studies, they suggest that the first multicellular organism must have lived as long as 1.5 billion years ago. The oldest fossil that we could argue as truly multicellular, however, is about 1.2 billion years old. More convincing fossils don’t appear until as recently as 600 million years ago.

When multicellularity arose isn’t clear, but its significance is much clearer. It enormously expanded the potential for evolutionary diversification that organisms could explore. It did so for a number of reasons. First, a single organism could now be composed of many cells, each of which could specialize for a single function. In other words, selection could act in different ways on different cells so that they could become more specialized. Cells could do just one thing very well within the amalgamation of cells in the organism.

The evolution of multicellularity also allowed organisms to become larger, much larger. Through the first couple of billion years of evolutionary history there are few if any organisms that you can see without a microscope. Once multicellularity evolved, organisms could become very large. In doing so not only could they become large complex things like blue whales, but more significantly and fundamentally, they could create an internal environment. This environment within the amalgamation of cells was much more favorable than the harsh external environment that they otherwise would live in. This allowed the specialization of cells on the outside of the organism to deal with harsh environments.

Perhaps the most significant consequence of multicellularity was that certain cells within an organism’s body had to become specialized for sexual reproduction. With single-celled organisms all we need is mitotic division. The evolution of specialized reproductive cells was something that had to happen, though, when we have a number of cells with different specialized functions. Some of these cells had to be sequestered and saved specifically for the task of making more individuals. Also, a different kind of division process must have evolved. This is the process of meiosis, which creates enormous potential for genetic diversity through recombination.

With the advent of sexual reproduction and the genetic variation that is a consequence of it, there was an enormous opportunity for evolutionary change.

If we reduce the entire history of the planet Earth to the scale of a single calendar month, the appearance of multicellular organisms would occur somewhere around the 24th day. Most of the month has already passed by the time has made it past single cells. From this point on, however, things accelerated very rapidly. Life increasingly became adapted and diversified into the untold forms that we see today.

There’s so much we can talk about in this regard, but I’ll leave that for another time.

A History Of Life, Part III

Not so long after photosynthesis and cellular respiration evolved, organisms started to eat each other. Single cells don’t have mouths, so the only way that one cell might eat another is by physically engulfing it. As prokaryotes diversified and competition for limited resources increased, it made sense that some cells would want to start eating each other this way, because to do so would be a very efficient way to obtain a big package of organic molecules all at once. Odd as it seems, the evolution of eukaryotic cells may be largely the consequence of cells trying to eat each other and getting indigestion.

This idea is known as the endosymbiotic theory of eukaryotic evolution, and was first proposed by Lynn Margulis. The endosymbiotic theory suggests that at least two of the most important organelles found in eukaryotic cells originated when one prokaryote engulfed another, and instead of ingesting it, it developed a symbiotic relationship with it. The Greek root symbio means “living together”. Endo is “inside”.

To get to endosymbiosis, probably the first thing that had to happen was that the cell membrane of the original eukaryotic cells had to evolve to become more flexible. Once a cell has a flexible membrane, it would be able to fold its membrane around and engulf another cell. It would also be able to do other things, like invaginate itself so that it could make internal compartments. For example, an enfolding of a cell membrane is thought to have given rise to the nucleus of modern cells, by providing an internal compartment in which the DNA of the cell could be protected from other biochemical activities of the cell.

It’s not clearly exactly how the origin of the nucleus is related to the evolution of the eukaryotic genomes, but there is no doubt that the existence of the nucleus in modern cells is essential for the way in they manage their DNA.

A Win-Win Situation

Once cells had developed a flexible membrane, larger cells began to engulf smaller cells as a way to obtain resources. Lynn Margulis contended that it is possible that a small prokaryote occasionally became engulfed but failed to be broken down. The smaller engulfed cell would now be trapped inside the larger cell. Of course, this arrangement could only be maintained over time if both cells benefitted in some way from the arrangement. In other words, this arrangement had to be adaptive in some way to both cells.

The advantage to the cell that had been engulfed seems obvious. It is now living inside of a very nutrient-rich environment, much more so than the outside. What could be the advantage to the large cell, serving as a host to the smaller cell? Margulis argued that there would be an advantage if the cell that was engulfed happened to have a more adaptive set of methabolic pathways. There are two such pathways that had evolved: photosynthesis and cellular respiration.

Specifically, Margulis suggested that the evolutionary origin of the organelles called mitochondria, which are specialized for energy processing, occurred when a cell capable of cellular respiration became endosymbiotic with a larger cell that lacked these pathways. Cellular respiration is much more efficient in the way it extracts energy from the breakdown of organic molecules. These proto-mitochondria would benefit by having a buffer from the rest of the world and a constant supply of nutrients. In return, the engulfing cell gained energy that was produced by the engulfed cell.

Similarly, Margulis suggested that chloroplasts, which are organelles specialized in photosynthesis, originated when an early eukaryotic cell engulfed a smaller photosynthetic cyanobacteria. As natural selection acted to make the host cell and its endosymbionts more dependent, this confederation of cells would eventually be integrated into a single organism. This single organism was a eukaryotic cell.

The Evidence

Margulis was greeted with skepticism when presented her theory. Over the decades that followed, however, a growing body of evidence has accumulated to suggest that she had it exactly right. Something like this happened about 1.5 billion years ago. Much of the original evidence was circumstantial. For example, if you look at the structure of mitochondria or chloroplasts, you see that they have not one membrane surrounding them, but two of them. This is what you would predict if a cell had been engulfed and maintained its own membrane.

There’s also the interesting fact that mitochondria and chloroplasts have their own genomes. It turns out that they not only have their own genomes, but they replicate by cell division themselves. This means that when a eukaryotic cell divides, in advance of that, the mitochondria and the chloroplast themselves have to divide. When the eukaryotic cell divides, there’s enough chloroplast and mitochondria to go around. The eukaryotic cell itself does not replicate mitochondria and chloroplast, they replicate themselves.

The most interesting piece of evidence, though, has come from phylogenetic studies of the mitochondrial and chloroplast gene sequences. If you look at the structure of the gene sequences found in these organelles, you find that they resemble their presumed ancestors: cyanobacteria.

Another interesting thing is that they have evolved together with the eukaryotic cell. Although they carry their own genes, they don’t carry enough genes to live entirely on their own. The genetic function of a mitochondria is in part due to genes that it bears in its own genome, and in part to genes that are found in the eukaryotic cell’s genome found in the nucleus.

The last interesting twist in our understanding of the evolution of eukaryotic cells is to ask: Who were the progenitors? It turns out that genetic evidence suggests that the archaea, not the bacteria, gave rise to the engulfing cell that became the eukaryotic cell. The organelles that were engulfed, however, were bacteria. What that means is that after the initial division of life into two major lineages, the archaea and bacteria, there was a reintegration of those cells to form this chimera as an innovative complex cell. To be continued…

A History Of Life, Part II

During the early period in the history of life, an enormous number of different kinds of biochemical pathways evolved. These are what we today would call metabolic pathways. There had to be developed biochemical pathways to obtain energy, process food, build macromolecules and carry out the functioning of the cell. It’s clear that some of the biochemical pathways, which are still central to the functioning of the cells today, arose very early.

As prokaryotes multiplied and diversified, competition for limited resources must have led to the evolution of increasingly diverse ways to acquire materials from the outside. So, the early evolutionary history of prokaryotes is really the evolution of a variety of metabolic pathways, which in turn is really the evolution of proteins. All of these metabolic functions are mediated by protein enzymes, which are what are catalyzing the biochemical reactions.

This kind of evolution isn’t something we can observe in the fossil record, but it is something we can deduce from the analysis of the structure of macromolecules and the DNA that codes for them.

It’s clear that nearly all of the metabolic processes that we find in modern cells today evolved in prokaryotes before eukaryotes even appeared on the scene.

The evolution of one biochemical process in particular had an overwhelming effect in the subsequent history of all life on Earth. Because early prokaryotes must had been competing for organic resources that would provide energy, the evolution of a process that could tap into a new boundless source of energy would had been a tremendously successful adaptation. One such source of energy is sunlight.

The Miracle and Curse of Photosynthesis

Photosynthesis is a biochemical process by which the energy of sunlight can be captured and used to build sugars, which in turn store that energy for the cell. Photosynthesis also arose very early in the evolutionary history of prokaryotes. Because of the obvious selective advantage of this trait, those organisms that possessed it soon became a dominant force on the planet.

There are several different kinds of photosynthetic pathways existing in prokaryotes today. The most efficient kind of photosynthesis, which is found in modern plants and cyanobacteria, has an interesting property: its efficiency is coupled with the fact that it generates oxygen as a waste product. This means that beginning with the evolution of photosynthetic pathways, oxygen began to be produced in abundant quantities.

The fossil record and other evidence suggest that cyanobacteria probably appeared around or before 1.7 billion years ago. Beginning about that time, generation of oxygen increased as this photosynthetic adaptation increased. So, the entire atmosphere of the planet Earth transformed from one which had no oxygen in it to one that is composed of about 20% oxygen. What’s the significance of this? Oxygen is a highly reactive molecule that interacts with organic molecules breaking them down. The presence of oxygen proved to be an environmental disaster of global proportions for most of the organisms that lived before oxygen appeared, because they simply could not live and function in an oxygen-rich environment.

This was the key to how organic molecules could evolve in the first place, as you may remember from my articles on the origin of life. The theory that Miller tested in his famous experiment assumed that the atmosphere had to not have oxygen for life to arise. When oxygen appeared on the scene, that kind of spontaneous synthesis of organic molecules could no longer occur. Furthermore, those organisms that had evolved in a non-oxygen environment now had a very hard time.

The biochemical and physical adaptations of organisms that had accumulated up to that time couldn’t cope with the oxygen revolution, but a few kinds of organisms did evolve some mechanisms that allowed them not only to cope with it, but in fact to take advantage of it. Specifically, some organisms developed a completely different process for methabolizing energy. This is a process we call cellular respiration.

The methabolic pathways of cellular respiration actually take advantage of the presence of oxygen to enormously increase the efficiency with which energy can be extracted from organic molecules. The evolution of photosynthetic pathways radically and permanently changed the Earth’s atmosphere and the biological inhabitants living on it. In the long run, also, it made certain changes that were key milestones in the history of life. Notably, it increased the amount of energy that can be produced by cells in two ways. Cells had found a new fuel, the sunlight, and a better way to burn the old kind of fuel with cellular respiration.

This increase in the amount of energy available permitted cells and organisms to become ever larger and complex. Another positive consequence of the accumulation of oxygen was the development of a layer of ozone gas in the upper atmosphere of the Earth. Ozone absorbs the radiation that hits the planet, and in so doing it made it possible for organisms to inhabit environments that previously were unavailable to them, most notably leaving the water and entering a land environment. To be continued…

A History Of Life, Part I

“All living things have much in common, in their chemical composition, their germinal vesicles, their cellular structure, and their laws of growth and reproduction. (...) Therefore I should infer from analogy that probably all the organic beings which have ever lived on this earth have descended from one primordial form, into which life was first breathed.”
Charles Darwin, On the Origin of Species

Darwin’s view of descent by modification led him to the conclusion that there existed sometime in the very remote past an organism that is literally the universal common ancestor of us all. I’ve already written some articles about how life could have arisen from non-living matter, you may be interested in reading some of them. At some point in the remote past, life was somehow “breathed” into a primordial form. An entity appeared we’ll all agree was living. Once this entity had gained a foothold on life, it became the common ancestor to everything that has ever lived on the planet.

Exactly when this organism arose is uncertain, but we know a few things. We know that it has to be around 3.9 billion years ago, when the surface of the Earth was no longer been bombarded, and the crust of the planet had cooled sufficiently for liquid water to appear. Also, it had to be sometime before 3.5 billion years ago, which is the date of the oldest fossil cells that had been found so far. These oldest fossils are found in rocks in Western Australia. They’re actually quite advanced in their appearance, resembling certain kinds of modern bacteria, so most biologists assume that cells must have appeared even earlier than this.

Let’s review the characteristics of this first living thing. This organism was certainly a single cell. It had to have a membrane that created a compartment separating it from the rest of the world, allowing the accumulation of specialized organic molecules within. Among the organic compounds that made up this first organism there must had been complex polymers capable of catalyzing biochemical reactions, the kinds of reaction that would be necessary for this primitive cell to process materials, grow and divide.

The most specialized of these biological polymers must have been some kind of molecule that could not only catalyze reactions, but also serve as a template for making more of itself. In the earliest cells, this information probably was in some form of RNA. Later, some kind of genetic system was established in an RNA world. DNA then took over the role of storing and transmitting genetic information, while proteins took over the role of the functional molecule responsible for everything else the cell might do.

Without doubt, at this early period in time, the major effect of natural selection on this primitive organism was to refine its genetic system and to ensure that the different kinds of molecules within it would cooperate. There had to be some selection so that these different kinds of molecules (lipids, proteins, nucleic acids and sugars) would be able to specialize to do their own jobs in coordination with each other.

A Prokaryote World

By the time we get to the oldest fossils, evolution had established a recognizable cell, which is not too different from what might be a typical bacteria we find today. There’s a rich fossil record that continues from that period up to the present day. This fossil record makes a couple of things clear. First of all, it shows that when life did emerge, it emerged very rapidly and quickly filled the planet.

It also shows that only prokaryotic cells existed for about 1.5 billion years, until about 2 billion years ago. In other words, the more complex eukaryotic cells didn’t exist for quite some time. The early evolution of life was all in the context of prokaryotic cells. The fact that prokaryotic cells ruled the Earth for 1.5 billion years might sound boring, but it’s nothing of the sort. There were at least two major and exciting evolutionary events that occurred during this period.

The first was that the prokaryotes themselves split into two major lineages. We call these the bacteria and the archaea. The differences between bacteria and archaea are relatively subtle in the modern world. There are biochemical differences in their internal composition and other things. In fact, there are enormously more bacteria in the world today than there are archaea. The archaea largely have been relegated to very extreme environments. These are the ones that we find in extremely saline water, for example.

In a sense, archaea are not necessarily an important form of life to understand today, but they are very important for understanding the origin of eukaryotic cells, as we’ll see later.

The Origin of Life, Part IV: Genetic Code

Ok. We’ve shown that it is possible for cell-like structures to spontaneously generate in certain conditions. How do we get from protobionts to all the enormously complicated and diverse stuff that we see today? We don’t know the answer to that question and we probably never will. We do know, however, part of the answer. Part of the answer has to do with reproduction.

How does a living system reproduce? What minimally do we need to get reproduction? How reproduction arose is an especially tricky problem. It is the problem that is most debated today in the area of the origin of life.

To understand what is needed for reproduction, let’s imagine we’re back in time. Let’s imagine we have some proto-cells that are functioning. Let’s say that by chance, one of these protobionts just happens to come up with some unique new trait. This trait could be anything. For example, it could be a new kind of molecule that makes this cell more durable. It could be a new kind of molecule that increases its ability to take up material from the outside.

This protobiont is different from the rest. It is somehow more efficient, better at doing its job. The problem is that we have only one of them. That individual won’t last forever. Even if it does, there will only be one of them. This issue leads us to reproduction. This problem would be solved if our protobiont could reproduce itself in a way that would pass that useful trait on to its progeny. How does it do that? Well, cells split into two. We have one cell, it grows a little larger and splits into two. In essence, that’s reproduction. This is not enough, however.

The Genetic Code and the Problem of Replication

If the trait we are talking about is a molecule, which of the daughter cells gets the molecule? Even if there is a lot of these molecules and each daughter cell gets a half of it, and the daughters of these cells get the half again, eventually this property will fade away. What we need instead is for these primitive cells to somehow be able to make completely new and accurate copies of themselves. They have to be able to store information about the structure of the molecule and transfer that information to its offspring.

How such a mechanism for storing and transmitting this kind of information came about is one of the unresolved questions about the origin of life. We know, however, that there is such a molecule in modern cells. This is a cell that accesses a blueprint for making more molecules. This molecule is called Deoxyribonucleic acid, or DNA.

DNA passes its information onto another kind of nucleic acid, RNA, and then the information goes from RNA into proteins. This is the way information works in modern cells. In this system, DNA acts as some kind of blueprint, RNA as the translator and proteins are the product of that blueprint. Proteins do much of the real work in modern cells.

Here we encounter a really serious problem, however. DNA could not have been the storage molecule that first arose in early life. Why not? The reason is that DNA can’t replicate itself. DNA requires a huge number of other proteins acting as enzymes to replicate. DNA in modern cells can be replicated but only if there are proteins to do the replication job. Proteins that could do that replication job might have arisen sometime in the early history of life on Earth, but they couldn’t have arisen before there was DNA to store their code. We need to postulate simultaneously the appearance of DNA that could store information about proteins and proteins that could replicate that DNA. Which came first, the chicken or the egg?

Neither could have come first because DNA and proteins can’t exist without each other in modern cells. Also, it is unbelievably improbable to think that just the right kind of proteins and just the right kind of DNA happened to arise spontaneously sometime in the early history of life.

What was need, instead, is for some kind of molecule that could do both of these things. A molecule that could replicate itself and it could do other useful things in the cell. Today we’re beginning to think that when life arose the molecule that did that was the nucleic acid RNA, or some early form of what we know today as RNA. Why we think that?

The RNA World

At the beginning of the 1960’s researchers have begun to suspect that RNA might have acted as the first blueprint or genetic material. In the laboratory, it is possible to put in some kind of RNA and then some building blocks, and under the right conditions the RNA replicates itself. RNA in the solution somehow acts as a template that helps the monomers come together in the right way and also polymerize.

A second breakthrough that led people to think that RNA might be the first information processing molecule came in 1983, when Thomas Cech actually discovered that, in modern cells, there are some kinds of RNA that do act as catalysts the way protein enzymes do. That is, they perform some important biochemical tasks in the cell. They are generally called ribozymes.

The important point is that these rybozymes are functioning as catalytic molecules just like protein enzymes. We’ve got two things now. We’ve got evidence that RNA can replicate itself and also evidence that RNA can have some sort of catalytic function. Taken together, these two sets of results suggest that in the very early stages of life, that magical point where a non-living protobiont somehow slipped over the edge into the state that we might want to call a living cell, happened in what we now call an RNA world. RNA actually dominated as the key biological molecule.

At some point after the RNA world, things changed. RNA had gotten the system rolling, but eventually DNA and proteins took over. DNA took over the job of being the information-bearing molecule. Proteins took over the job of doing all of the catalytic and other kinds of work in the cell. RNA became relegated to just an intermediate in the process.

Why this would happen is fairly obvious. Proteins are extraordinarily versatile molecules. They do an enormous number of tasks. Their versatility comes from the fact that they can assume all sorts of complicated shapes in a way that RNA can’t. Proteins clearly took over doing the real work in the cell because they were really good at it. DNA assumes a particular kind of chemical configuration that makes it really good at storing information in a way that RNA is not particularly good. Once we have DNA, it is much better than RNA at making more copies of itself and storing that information. So, it took over that job. RNA became just an intermediate.

I think that with this we have what is basically needed to the appearance of life. We’ve explained the origin of life, at least in part. Quite an accomplishment, eh? How do we get from these simple cells to platypuses and other things is another subject, and don’t worry, I’ll try to tackle it.

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The Origin of Life, Part III: Primitive Cells

The experiments of Miller, Fox, Ferris and others had shown that complex polymers could arise spontaneously on the early Earth. We know, however, that the organic molecules that make us up are not just a jumble of things floating around in a primordial soup, they are highly ordered. They come in highly ordered packages. There are many such packages in living systems, but the most fundamental one is what we call the cell. All living things are made of units called cells. Minimally, for something to be living, requires a barrier between the living part and the non-living part. That barrier is what would define the cell.

Is it possible that some cell-like structure could arise spontaneously on the early Earth? Here, too, laboratory experiments suggest that the answer is yes. A number of experiments have been done that demonstrate, under conditions that are not too rigorous, that you can get aggregations of molecules that would spontaneously form cell-like structures.

This kind of spontaneously made cells are called protobionts. You can actually make protobionts, it is not difficult to do. You can make them under a number of different kinds of conditions. For example, if you have the right kind of lipids, you can almost literally put them in water and they spontaneously form a package where there is a membrane of lipids that encloses some central space.

The most remarkable kind of protobiont, called coacervate, is one that has been made to self-assemble out of a solution that includes polypeptides, nucleic acids and polysaccharides. If you have the right conditions, you can make these to self-assemble into a cell-like object. What is really interesting about coacervates is that if you then throw into the mix some real biological molecules, a protein enzyme that you’ve taken from a real living cell, for example, the coacervates can take up those enzymes. They would bring them inside of themselves.

Those enzymes would start working inside the coacervates. What enzymes do is to process some kind of biological molecule into another. Once these enzymes have been taken up by these coacervates, it would also start doing the reactions and putting out the products. This is really getting remarkably close to something that we might want to call living.

I don’t say that we can make primitive cells. Nobody has actually made a cell that any biologist would look and say “oh, that’s a cell you just made”. People are trying to do that now, but it hasn’t been done yet. We can, however, make cell-like things and it doesn’t seem to be any big trick. These things spontaneously form, we know that for sure.

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The Origin of Life, Part II: Polymerization

Okay, let’s go on with the origin of life. In my last post I talked about Miller’s experiment. The significance of this experiment was simply to show that non-biological processes could result in the formation of organic molecules, including amino-acids and nucleotides. These molecules that Miller got, however, were still relatively simple. They thus only represented a first small step.

Amino-acids and nucleotides by themselves don’t get us very far because we need to get these simple molecules linked together. They act as building blocks to make the more complicated stuff that we are really made up of. The technical term for this process is polymerization. In other words, complex organic molecules, like proteins, or DNA, are polymers. They are long chains of building blocks(monomers).

Miller was able to make the building blocks, but living things need those building blocks strung together in polymers.

Ordinarily, in living things today, there are a series of specialized proteins, called enzymes, that are responsible for building these polymers out of the monomeric building blocks. What happened in the early Earth in the absence of these specialized protein machinery that could possibly lead to polymerization?

Polymerization in Laboratory

The first evidence that this was possible came fairly early on in the late 1950’s, and it was worked by Sidney Walter Fox. Fox took Miller’s experiment one step further. He was able to take amino-acids that might have been created in an experiment like Miller’s and get them to start joining together but only under certain conditions. In just the right proportions, in just the right temperature, the right amount of time that you might heat them, he could get short polymers of amino-acids. We call a polymer of amino-acids a protein, but we also call it a polypeptide chain. That’s simply because the chemical bond that link these monomeric amino-acids to form that chain is called a peptide bond.

What Fox was able to do is to get fairly short polypeptides, showing that you can get spontaneous polymerization. The problem was that Fox could only do this under a very narrow range of conditions. In Miller’s work, you could just throw a bunch of stuff into those flasks, and you get some sort of organic molecule. Fox’s work, however, required much more controlled conditions, conditions that are unlikely to have been that of the early Earth.

Origin in Clay?

Fox and a number of other scientists, however, speculated that maybe you could get more spontaneous formation of polymers if you had some sort of non-biological catalyst. A catalyst is just a term that refers to something that makes a chemical reaction run faster. What Fox and others suggested was that maybe there was something that was non-biological that could catalyze these polymerization reactions. Specifically, what they suggested was that perhaps there were certain kinds of clays that acted as inorganic catalysts.

Why clay? It turns out that some kinds of clay, when they dry out, form very regular ladder-like structures. Furthermore, these clays would also have weak electrical charges on their surfaces. These weak electrical charges can adhere organic molecules. The idea here is that sometime in the early Earth, the shores of a primitive ocean had a bed of clay. As organic molecules that were being created in that primitive ocean got accumulated into the shore, they adhered to that clay. And the clay, because of its regular order and the spacing, would increase the probabilities that you get some sort of spontaneous polymerization.

Wow, that’s an interesting idea. Is there any evidence that this could work? We don’t know what the primitive Earth was like at that scale, but it turns out that recent work by James Ferris, who is at the Rensselaer Polytechnic Institute, has shown exactly that this process does work under abiotic conditions. In a laboratory, Ferris and his colleagues have been able to synthesize not only short polypeptides, but also short stretches of DNA from the component building blocks that were created from experiments like those done by Miller.

The proteins and DNA that Ferris and other have produced are not functional. These are strings of monomers that have been polymerized, but they don’t make any sense. It’s not like a string that would do anything like a real biological molecule might. Nevertheless, it is a start. We can postulate that biological polymers could arise spontaneously.

So, let’s imagine that we have complex polymers. Let’s imagine that we’ve got a primitive ocean brimming with a whole bunch of organic polymers, what has been called the primordial soup. Let’s imagine that even some of these polymers, by chance, have come together as strings that might even have some sort of useful biological function, like modern polymers. Where do we go from there?

The experiments of Miller, Fox, Ferris and others had shown that this is possible, but even with all of this we still don’t have anything approaching what we would want to call life. Why not? Because we know that the organic molecules that make us up are not just a jumble of things floating around in a primordial soup, they are highly ordered. They come in highly ordered packages. This is going to be the subject of my next post, cells. Stay tuned.

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The Origin of Life, Part I; Miller's Experiment

As Richard Dawkins puts it, “the theory of evolution is about as much open to doubt as the theory that the Earth goes round the sun”. We can also be sure that all of the diverse forms of life we see around us today have arisen from some common, primitive, single original living entity. Our first problem is, then, how this living “thing” originated. In 1953, Stanley Miller conducted his famous (or infamous) experiment. At the time he was a graduate student at the University of Chicago. For decades, scientists had speculated whether the complex organic compounds characteristic of living things could have somehow been generated spontaneously on the early Earth. Spontaneous generation of organic compounds can’t happen today. This is because organic compounds are too fragile.

It is possible that, given enough time, a complex compound might just come together. If it did, however, it would immediately be taken apart. This is because today our planet is just filled with oxygen. Oxygen breaks down organic compounds. Oxygen pulls electrons out of organic compounds and turns them into inorganic compounds.

How can we even get the formation of any kind of organic compound, if as soon as anything begins to arise by chance, it is immediately taken apart? Well, this one is easy. If oxygen is bothering you, just get rid of it.

Before the Miller-Urey experiment, two scientists, Alexander Oparin and J.B.S. Haldane, independently suggested that the early Earth actually did not have much or any oxygen. Oxygen is all around us in the atmosphere, but they suggested that when the planet was formed, the first atmosphere that developed was entirely composed of just a few gases: hydrogen, methane, ammonia and water vapor. This would be as the atmospheres of the moons of other planets that have been described.

Oparin and Haldane independently suggested that the problem of spontaneous generation of organic compounds wasn’t really a big deal, because the early Earth did not have an oxidizing atmosphere. To test this hypothesis, what Miller did was set out to reproduce the conditions presumed to exist on the early Earth before life have arisen, and see if he could get the spontaneous production of organic compounds.

A Simple Experiment, Powerful Results

Miller’s experiment was set up this way: He had two flasks connected by a series of glass tubes. He had a lower flask in which he put water, and he heated this water gently with a little flame. He would cause the water to evaporate and create water vapor, which would circulate into a higher flask. In the upper flask, Miller also added a number of other gasses. He created an atmosphere similar to the one of the early Earth, consistent of hydrogen, methane, ammonia and wáter vapor.

The Experiment. Souce: Wikipedia.

Miller also exposed the gases in this upper chamber to a lot of energy by putting two electrodes that would create electrical sparks. He knew that he needed energy to create any kind of compound, certainly organic compounds.

This is actually a pretty simple experiment, and you can almost do this in your own house. All of these materials are easily available. You could replicate Miller’s experiment and results, which were spectacular. In only a couple of days, he found he could synthesize a whole range of different organic compounds, including some very complex ones, like amino-acids.

The scientific community immediately set out to replicate this. Many people replicated the experiment and it quickly became clear that depending on starting conditions, it was possible to spontaneously, without any preexisting organic molecule, produce all of the amino-acids that are normally found in living material. Most intriguingly of all, you could create nucleotides, which are the building blocks of nucleic acids, DNA and RNA.

The implication of Miller’s experiment and those that followed was that there appeared to be no trouble at all for complex organic compounds to arise spontaneously on the inorganic early Earth. This is a first stepping stone to the origin of life from non-living matter.

On the other hand, as exciting as this result was, the organic compounds that Miller created were still relatively simple compared to the stuff that we are made of. What else do we need to get something that we would call “living”? We have to take our synthesis of organic compounds even farther, beyond these organic building blocks, to get the varied extremely complex molecules that living systems are really made of. We will see how that was possible in the early Earth next time.

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In the Beginning

In the beginning... there was a singularity. Physicists tell us that the universe, as we know it, began between 10 and 20 billion years ago, at a moment in time they call the Big Bang. Our own star is comparatively young. Estimates are that it formed about 5 billion years ago. As our solar system was forming, cosmic dust gradually got swept up and began to form planets. Scientists estimate that our own planet reached its present size at about 4.6 billion years ago. That is generally taken as the age of the planet Earth.

In the beginning, planet Earth was a really miserable place. The way that the planet was formed, with ever larger and larger chunks of material slamming into it, created an enormous amount of heat. When the planet first formed it was melted. It was no place where one could ever conceive of life existing. Less than a billion years later, however, the fossil record clearly shows that life was there. This life was in the form of simple cells that resembled the bacteria we see around us today.

This is pretty fast work, especially when you consider that it took about a half a billion years just for the Earth to cool enough to actually have rocks and an atmosphere. In fact, some scientists now argue, based on fossil evidence, that life might have been present even earlier, as earlier as four billion years ago.

What we can take from this is that life appeared on the planet almost as soon as it was possible to do so. As soon as there were rocks to record the existence of life, we find evidence that life is there.

Where do these organisms come from?

In the beggining, life originated on the early Earth from non-living materials. All of the diverse forms of life we see around us today have arisen from some common, primitive, single original living entity. This is pretty deep stuff, a very cool idea.

There are alternatives to this account, of course. Many religious faiths hold that, in the beginning, life was bestowed on the planet by the work of a deity, but this is a pretty boring idea. Another alternative, one that has been suggested repeatedly over the years by a number of scientists, is the panspermia hypothesis. It suggests that the first life on Earth came from somewhere else in space.

Both of these alternatives, however, beg the question of how living matter could arise from non-living matter. That brings an important question into the table.

What’s the minimal difference between living and non-living materials? This is basically the same as asking “what is life?”. This question has been around for a long time. For me, however, with all the knowledge we have today at our disposal, to address this question is pretty simple.

So, what is life?

Life is defined by what is called organic chemistry. The most fundamental difference between living and non-living matter has to do with chemistry. Living things all have in common the fact that they are made of a particular class of chemical compounds. These are compounds that are built around the unique chemical properties of the element carbon. These kinds of compounds are called organic compounds. They are called that way because they are uniquely associated with living organic things.

There are only four kinds of organic compounds, broadly speaking. The first kind are amino-acids. These are the things that make up protein. The second kind of organic compound are the nucleic acids. These nucleic acids are DNA and RNA. The third class are the carbohydrates. These are what we commonly call sugars. The last general class of organic compounds are the lipids. Lipids are what we commonly call fats in many cases, but lipids can actually take a number of different forms.

These organic compounds have particular and quite sophisticated chemical properties that are unique to them. There is one property that is particularly remarkable, that is that the complex organic compounds that we find on the planet today, the stuff we are made of, is generally only produced through the action of living things. Another way to put this is that the creation of new organic matters depends on the existence of organic matter. You can’t make more organic compounds unless you got compounds to make them.

We can be quite confident given what we know about how the planet was formed the early Earth was entirely inorganic. Then, we have to ask: Where did the organic compounds that life depends on came from in the beginning? At this point, you might think that I’m going to throw Intelligent Design and Creationist arguments at you. I won’t, don’t worry. I’ll create some tension and leave that question unanswered, until next time, when we talk about the exciting, random and unintelligent origin of life.

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