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.