Extended Universe

December 1, 2011

One of the greatest events in the history of Areiosan life was the advent of eukaryotic life. And this undoubtedly couldn’t have happened without the advent of mitochondria. Mitochondria are organelles within our cells that generate ATP, the energy currency of our cells. This process of ATP synthesis requires oxygen and produces carbon dioxide and water as waste products. Every complex animal on Earth uses this biochemical pathway by the virtue of their collective mitochondria’s electron transport chain. It is clear that without mitochondria, life on Earth would look very different. The origin of mitochondria on Earth as on Areios marks a profound threshold in the geological record; the rise of mitochondria presages the arrival of multicellular life.

Mitochondria in eukaryotic cells produce more energy through oxidative respiration than their anaerobic brethren, and multicellular life profits from this by investing that additional energy in development, growth, movement, and complexity. The number of mitochondria found in a eukaryotic is strong indicator of the kind of activity that specialized cell performs. Our muscle cells enjoy a much higher density of mitochondria than our blood cells, for instance. This is because our muscles cells require a tremendous amount of energy to move our bodies. Without mitochondria, complex life forms like animals almost certainly would have never emerged. Mitochondria in our cells are like microscopic power plants that provide energy for our cells. Without them, there simply isn’t enough energy in microbial metabolism to provide enough juice to power any complex animal.

Through this endosymbiotic event, all complex life was able to emerge. So the origin of mitochondria is fundamental to our understanding of the origin of complex life on Earth. As discussed in an earlier, researchers believe that a rickettsia bacterium was swallowed by another predaceous cell and survived; a mutualistic relationship occurred between the host and the rickettsia that evolved into the current configuration in our cells today. An archaean cell could have lost the genes that code for its cell wall. Without a cell wall to hold it back, this cell could live free  with only a cell membrane keeping its cytoplasm separate from the rest of the outside world. This archaean cell would be able to fold onto itself and swallow other cells whole instead of filter-feeding organic molecules that floated nearby. Somehow, it ingested a live cell that didn’t get broken down by lysosomes or digestive enzymes. And this stowaway was useful; it could reduce any toxic oxygen molecules in the cytoplasm that would otherwise poison the archaean cell. This mutual relationship persisted for millennia until the engulfed cell became nothing more than a stripped-down set of genes responsible only for a select set of chemical pathways. This wasn’t the only endosymbiotic event in the history of Areios; there were three events that led to the rise of eukaryotic life.

There were two endosymbiotic events that transformed a new kingdom of life on Areios before the advent of mitochondria that led to animal life. First, a virus that failed to infect a bacterium evolved a mutualistic relationship that culminated in the creation of the first nucleus. The virus hijacked the cell’s DNA, but was unable to use the cellular machinery to replicate itself. Eventually, the virus’ protein coat served as a citadel for the cell’s genetic material against future viral sieges, making it harder for future viruses to infect this proto-eukaryotic cell. The virus’ protein coat would become the cell’s nucleus, directing the cell’s biological activities from a fixed, centralized location bound to the cell membrane. The second endosymbiotic event occurred when a sulfate-reducing organism was engulfed in another bacteria cell. Not only could organism detoxify the environment within the cell by converting sulfur compounds into useable forms, it could store those sulfur compounds internally and release them when food availability for its host was poor.

The final endosymbiotic event in Areiosan history created the mitochondria. This event parallels a similar that occurred on Earth; an organism that that can convert peroxides into water by reducing oxygen gets engulfed by a bacteria and sweeps the toxic peroxides out of the cell. Eventually, this process gets exploited by the host cell for making sugars because the process of reducing oxygen in the electron transport chain is so energetic. That electron transport chain in mitochondria is ubiquitous for animal life; it’s the power source for our ability to grow, move, reproduce, and maintain our cellular complexity.

 

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Endosymbiotic Universe

November 8, 2011

Endosymbiosis occurred two separate times in Areiosan history. Part of the reason why animal life took so much longer to form on Areios is that two separate endosymbiotic events had to occur before the creation of mitochondria. The first major endosymbiotic event occurred when an errant virus was engulfed in an episode of transduction gone awry. Transduction is one way that viruses infect cells, stealing into their cytoplasm and hijacking the cellular machinery of the host cell to make copies. Somehow, this process was disrupted and while the virus had infected its host cell, it couldn’t wrest control from the cell’s RNA to make virus proteins. This cohabitation eventually proved to be a great opportunity for the cell because in the transduction event some of the virus’s DNA was mixed with the DNA of the host germ. What resulted was a fusion of the nucleic material of the virus with the nucleic material of the host. One of the biggest effects of this synthesis was the compartmentalization of the DNA from the rest of the cell. In bacteria, DNA is a free-floating piece of cyclical DNA that is exposed to the chemical reactions occurring inside the cytoplasm. By cordoning off the DNA, this cellular experiment provided a safer environment and offered an added bonus; other viruses had a harder time cracking the defenses of cells with nuclei. Although it started as a botched attempt at usurping a cell’s reproductive ability, this primordial endosymbiotic event ended with the creation of a new form of life.

The next endosymbiotic event was strongly influenced by environmental change. Oceans were becoming more acidic with the build-up of sulfur dioxide in the atmosphere that led to sulfuric acid raining down on the oceans. The rise of acidophiles in oceans sucked up the sulfate swashing around in the ocean when sulfuric acid dissociated. By intaking that sulfate and picking out the methane that dissolved of the ocean, these acidophiles could metabolize these inputs while excreting bicarbonate ions and reduced hydrogen sulfide gas. Living in such acidic environments would cause acidophiles to evolve mechanisms for thriving in conditions that would prove lethal for many other organisms. Acidophiles do this by pumping hydrogen ions out of their cytoplasm, so any organism that could hide inside of an acidophile would live in an environment that is much closer to a neutral pH than the oceans. Another issue that would prove daunting for life was that with pH dropping in the oceans, soluble toxic metals were getting leached from the geology and dissolved in anoxic environments, further poisoning any organism not adapted to living in brine laced with heavy levels of iron and other transition metals.

Nitrate levels are higher on Areios because nitric acid formed in the atmosphere and would dissociate into hydrogen and NO3. This acid would dissolve into the oceans and prove poisonous to Areiosan acidophiles as well. So an organism similar to the Beggiatoa species on Earth appeared that was primed to overcome this dilemma. Not only can Beggiota metabolize nitrate and hydrogen sulfide to form waste products like ammonia and sulfate, but it can also store sulfur intracellularly and use this elemental sulfur as an energy source in the presence of oxygen to form sulfate. Originally, Beggiaota formed an endosymbiotic relationship with an archaean acidophile because Beggiaota could use any oxygen that enters the acidophile and burn its store of intracellular sulfur. Plus, it could store sulfate for times when sulfate levels dropped and release it into the cell when the concentration of sulfate in the host cell dropped. Here, a symbiotic relationship occurred where the acidophile lowered the survival costs of the Beggiaota by giving it safe harbor and in exchange, Beggiaota would provide a food source for the acidophile during times when food was scarce and eliminate any toxics that crept into its intracellular environment.

But when the oceans became more acidified, Beggiaota took on another purpose as well; it could take in nitrate from the environment and turn it into ammonia. Ammonia is a powerful base and when it comes in contact with the acidity of the ocean, it would form a salt that neutralizes the ocean. The emergence of this early eukaryote profoundly manipulated the chemistry of the planet; as time progressed, the composition seawater changed as dissolved chemicals like sulfate, nitrate, methane and hydrogen sulfide were replaced by chemicals like bicarbonate and ammonia. This profoundly altered the biosphere and the composition of the atmosphere because it brought the pH of the planet back up to neutral after the build-up of gases in the atmosphere from outgassing dropped the pH. This constant battle between acids and bases is evidenced by the near-constant salt concentration in the Areiosan Ocean since the advent of eukaryotic life.

 

Engulfing Universe

September 5, 2011

The first eukaryotic organism on Earth sported a novel invention; the nucleus. In prokaryotic cells, the nucleic material that is responsible for regulating cell function is a free-floating cyclical strand of DNA. It wasn’t until the advent of the nucleus and membrane-bound organelles that the first animal life appeared. Molecular biologists have proffered that membrane-bound organelles are the result of a faulty gene that eliminated the prokaryote’s rigid cell wall. The fluidity of the cell membrane allows for sections to flop around and fold back onto itself, forging innovations like the nucleus, the endoplasmic reticulum and the Golgi apparatus of our eukaryotic cells. Areiosan eukaryotes contain membrane-bound organelles similar to the ER and the Golgi, and while collectively these two Areiosan organelles can accomplish the same tasks as the ER and Gogli, the division of labor is wholly different from our cells.

The origin of the nucleus is thought to be accident; some have proffered that it all began with a virus. Viruses are rudimentary biological machines that aren’t even alive because they cannot reproduce on their own. Made of a strand of nucleic acid surrounded by a protein coat, a virus hijacks a cell’s ability to reproduce and infects a cell to commandeer reproduction. The origin of the virus is unclear; one hypothesis suggests that they may have evolved from plasmids, extraneous pieces of DNA get traded back and forth by bacteria in a process called lateral gene transfer. Another theory claims that viruses may trace their origins back to parasitic cells that loss much of their cellular machinery, eventually becoming a barebones reproduction machine. In general, though scientists suspect that virus may trace their origins back to a primeval time before the emergence of archaea, bacteria, and eukaryotes. Nonetheless, even though they are generally thought to be rudimentary, some viruses have been known to contain more nucleic acid within them than even some smaller cells.

The current thinking about the origin of the nucleus is that some hapless virus infected a bacterium, but through luck or some other cause, the virus did not succeed in replicating itself and taking over the cell. Or perhaps a cell unwittingly swallowed virus, engulfing it in phagocytosis. In either case, in order to reproduce, viruses have to infect a healthy cell and take over the cell’s machinery in order to reproduce. Stranded inside the cell, but unable to take the cell over or to reproduce itself, the virus has taken over control of the cell’s RNA molecules, which allow it to make proteins. But, while it has usurped the bacteria’s DNA for control of the cellular processes, the virus is stuck regulating the workings of the cell. Over generations, the virus lost genes responsible for infection and shed some of its protein coat that eased the transmission of genetic material into the rest of the cell. From here, it is easy to conceive of a proto-nucleus; the virus has control of the RNA’s inside the cell, it is tangled up in the cell membrane, it has lost the capacity to infect other cells, yet it can’t be expelled or destroyed from within the cell by any immune response. This arrangement persisted for eons until the virus resembled something like a rudimentary nucleus.

The endoplasmic reticulum of a cell is a series of membrane-bound sacs that are involved in biosynthesis of certain molecules. The ER comes in two varieties, the smooth and rough ER, which is determined by the presence of ribosomes stuck to surface. In eukaryotic cells, the ER is responsible for processes that normally take place in the plasma membrane of a prokaryotic cell, like synthesizing proteins, lipids and steroids or metabolizing carbohydrates. By no stretch of imagination, one could hypothesize that the smooth and rough forms of the ER arose from an invagination of the plasma membrane that broke off and became specialized. For instance, while a plasma membrane is capable of functions like exocytosis and endocytosis that takes in and spits out macromolecules, the ER does not have that function.

Similar to the ER, the Golgi apparatus is another membrane-bound organelle that modifies macromolecules. The Golgi complex manufactures lysosomes and tags certain molecules with a carbohydrate or phosphate marker so those molecules can be sent to a specific location within the cell or removed by exocytosis. The Golgi apparatus likely formed as the result of invagination of the cell membrane to form a tube-like organelle that could later form vesicles for packaging molecules.

Ensconcing Universe

July 16, 2011

Where do Eukaryotes come from? The distinguishing feature of eukaryotes is the stately nucleus that adorns every eukaryotic cell. The best theory to explain how nuclei came to be is called the endosymbiotic theory. The origin of the earliest eukaryotic cells was one of the leading mysteries in biologist, but the researcher Lynn Margulis offered a compelling solution to this enigma with her endosymbiosis theory. The theory can adequately explain many mysteries about the origin of the Eukaryotic domain. While much the process remains elusive, scientists believe they have a fairly accurate conception of how the first endosymbiosis occurred. Some archean bacteria have a rigid cell wall that keeps its shape, but at some point, this cell wall disappears in a certain archean lineage. Through either a faulty cell wall gene or a complete excision of the genes that controls cell wall production, a cell’s insides were no longer boxed in by a cell wall and the only thing keeping the contents of our cell from leaking into the outside world is a tenuous cell membrane. This underlying cell membrane is fluid and allows cells’ edges to fold in on themselves, creating bubbles called vacuoles. Rather than sucking in dissolved chemicals through the cell wall, this archean cell can engulf cell fragments and even whole smaller cells by folding itself over the cell to be eaten, and then pinching itself off to form a vacuole around it. This process is called phagocytosis and it engulfs macromolecules in vacuoles.

 

An archaean cell like the one described above could flop around without a cell wall and fold over its food to eat. One of these archaean cells swallowed a living a bacterium that managed to survive in the cytoplasm of the cell that ate it. This bacterium somehow was kept from being digested by a lysosome within the host cell and lived long enough to replicate with the host cell time and time again. Eventually, this bacteria found a nice little home within the archaean cell, living sheltered from the dramatic changes in the environment that the archaean has to face. Scientists tend to think that the unlucky bacterium that got engulfed was a rickettsia bacteria; this is important because rickettsia can detoxify peroxides into water. Peroxide is a free radical inside cells, hacking apart the cellular machinery and the rickettsia is useful for the archaean cell because it takes a poisonous chemical and turns it into water. This process repeats itself on Areios, creating the first eukaryotic cells by endosymbiosis.

 

Because the engulfed cell relied on the host for maintaining homeostasis, mutations or deletions in its genome for certain biological pathways could get destroyed without impacting the cell’s ability to reproduce. For instance, lodged inside another cell meant that genes responsible for locomotion could erode without hurting the viability of the engulfed bacteria. Eventually, the engulfed cell lost much of its cellular mechanics and diminished in size until it was no smaller than an organelle. Yet unlike other organelles, like mitochondria and chloroplasts, which were created by this process of endosymbiosis differ in two unique ways. First of all, they house DNA inside of a cell yet outside of the nucleus where DNA is ordinarily kept. And two, they have a membrane that shuts them off from the rest of the cell that is wholly different from the cell membrane that separates the cell from the outside world.

 

Endosymbiosis has occurred several times in the history of eukaryotic cells as seen in euglenas and other protists that have more than one membrane surrounding their organelles. This is evidence that a proto-euglena swallowed an alga, and a secondary symbiosis had occurred in that family. This would give the euglena’s mitochondria two membranes surrounding it; the original membrane that surrounded the mitochondria of the alga, and the second cell membrane came from the alga itself that went through the same process described above, where its genome and machinery could get whittled down until just the cell membrane remained.

The earliest eukaryotes could have arisen from a symbiotic relationship with an engulfed aerobic heterotrophic prokaryote

Edible Universe

April 27, 2011

After Areios unthawed from a 130-million-yer long period of worldwide glaciations, the planet looked remarkably different from before the deep freeze. The atmosphere was made up of reduced gases like water vapor carbon dioxide, hydrogen sulfide and methane, and carbonyl sufide. Gases like water vapor, carbon dioxide, carbonyl sulfide and methane are powerful greenhouse gases that raise the average temperature of the planet. On Earth, an excess of these gases generated by human industry are widely believed to cause destabilizing climate change on Earth. On a planet like Areios, this increase in greenhouse gases is a boon because it melted the ice that straddled the tropical regions of the world and caused sea levels to rise, washing organic salts and other chemicals locked in the continental crust into the sea, making a frothy brew of organic chemistry that would form the basis for the earliest life.

Deep at the bottom of the ocean, there are volcanic vents that eject boiling water laced with metals; on Earth these environments are heavily populated with life. Meter-long tubeworms powered off of bacteria in their guts that eat the dissolved gases in the water. Translucent crabs and squids feed off of the see-through krill that are the basis of this underwater ecosystem. Researchers believe that the bacteria found in these vents are among the oldest known organisms on Earth. Similarly, these vents are the wellspring for the first life on Areios. Iron-bearing minerals at the bottom of the ocean serve as catalyst for complex organic molecules to form. Over time as a primitive form of natural selection takes place the more robust molecules that replicate with greater efficiency win out over organisms that can’t replicate fast enough or fall apart too easily. And over time, those molecules that could replicate the best would dominate the environment. It’s easy to imagine that the first life forms on earth were bare-bones, single-celled proto-cells that could replicate and do not much else.

Over time, those that developed a more robust metabolism could survive times when the organic molecules that they fed on were scarce. And as natural selection kept on, the metabolisms of these early cells became more and more eclectic, with many different metabolic pathways being developed by their forms to exploit the energy around them. This allowed for greater biodiversity and minimized competition for the same resources. The early biology on Areios as well as on Earth formed these microbial mats; an entire ecosystem was enclosed in a single patch of pond scum, with some creatures emitting gases like methane or hydrogen sulfide and other creatures that could exploit these waste for their own metabolism, transforming that hydrogen sulfide into sulfur granules of sulfuric acid and breaking that methane down into hydrogen gas that bubbled out of seas.

At first the earliest life was confined to a single area, but pressure for resources like the organic molecules that served as food, life forms began to spread out around the globe, filling up new unexplored niches and evolving to meet the new conditions. Eventually, every niche around the world was filled up and there was nowhere else for these life forms to head to. And from that point on, the competition for resources intensified and the less resilient creatures were muscled out of their niches. In perhaps the greatest phenomena of the time, predation arrived on Areios soon after the niches of the world were taken. Bigger organisms no longer had to engulf free-floating molecules in order to feed; they could engulf their free-floating cousins, too. This is entirely because of biological compatibility; organisms that ingest free-floating molecules incorporate nutrients into their metabolism and other organisms with the right cellular machinery can eat those cells and gain their nutrients from the primary producer. This was one of the first major events in the history of life on Areios and predation will lead to yet another milestone in the history of life; the appearance of eukaryotic cells from what is called endosymbiosis. But more on that later…

Early life may have formed in hydrothermal vent communities.