Envisioned Universe

March 5, 2012

Animals that breathe oxygen use a process called oxidative respiration to get their energy from the food they eat and respire or breathe out water vapor and carbon dioxide.  Oxidative respiration is a hallmark for all complex animal life, but there are many evolutionary steps between the advent of the first life form that breathes oxygen, which was singe-celled and the first true animal life, which might have millions or even trillions of cells.  Before the first animals could appear on Earth, a highly organized and complex system responsible for governing an organism’s growth and development was needed to make sure that all of an animal’s cells were arranged in the proper place.  Imagine a fruit fly with feet on its head, and this should give one some perspective about the importance of the genes that regulate growth and development in animals.  The growth and development of organisms is controlled wholly by a specific set of genes and how these genes are activated is a process called gene expression.  Gene expression is of paramount important for eukaryotic organisms because of the sheer complexity involved in the development process.  Single-celled prokaryotic organisms don’t need the same tightly-regulated mechanisms that are characteristic of eukaryotes, but when trillions of cells need to be organized in a coherent way, these genes must be able to step up and complete the task.

All animals on Earth share certain key characteristics, like the ability to use oxygen in respiration mentioned earlier.  To start, because all animals are eukaryotic, the DNA is contained within the nucleus of cells so the process of replicating DNA, called transcription, occurs within the nucleus.  In addition, the process of replicating proteins, called translation, occurs mostly in ribosomes, which are organelles found in the cytoplasm.  Compared to prokaryotes where the process of translation and transcription occur in the cytoplasm, eukaryotes undergo translation and transcription separately.  This is important for eukaryotes because by segregating these two processes, both translation and transcription become more efficient.  This is especially important for eukaryotic organisms because the genome of eukaryotes can be 10 to 100 times larger than the prokaryotic genome.  The DNA of eukaryotic cells is loaded with transposons.  Transposons are repetitive sequences of genetic material that are able to move a transposase gene around within the genome.  Transposase allows the DNA to loop around itself and cut off a piece of the genome and relocate itself somewhere else within that strand of DNA.  Wherever it lands, the excised transposon disrupts the function of the gene that was occupying that stretch of the DNA.  So transposons help to regulate when and where and how which of our genes function at any given time.

Our Areiosan life uses all of the same steps for genomic expression that Earth life does, but different proteins are responsible for regulating genomic expression because our hypothetical life would have evolved on a different world and would have been subject to a completely different environment.  A typical eukaryotic protein-coding gene is surrounded on both sides by what are called a promoter and terminator sequence.  A promoter sequence is located upstream of each gene and serves as the sign that identifies that particular gene to the enzymes that will latch onto to it.  The terminator sequence appears at the very end of the gene and marks the point on the DNA were an enzyme should stop coding and signifies where a certain gene ends. DNA is made up of two different kinds of sequences; sequences that code for a certain gene and sequences and don’t code for a certain gene.   Noncoding sequences within DNA called introns.  They appear on the DNA in between segments responsible for coding proteins.  The sequences of genes that are responsible for coding proteins are called exons.

The similarities that pop up between my Areiosan gene expression and Earth gene expression are twofold. One, I don’t have an advanced degree in molecular biology, biochemistry, or genetics, so the thought of making up a brand new system of gene expression is a daunting task, and I thought it would be best to go with what I knew, which was how this works on Earth. And second, I like the idea of unifying life. Even in an imaginary world that I made up, it’s comforting to envision similarities, especially with the creatures that I designed to be so alien to begin with. One thought that has been hanging around my subconscious for a while came from a physicist Lawrence Krauss:

“Every atom in your body came from a star that exploded. And, the atoms in your left hand probably came from a different star than your right hand. It really is the most poetic thing I know about physics: You are all stardust. You couldn’t be here if stars hadn’t exploded, because the elements — the carbon, nitrogen, oxygen, iron, all the things that matter for evolution and for life — weren’t created at the beginning of time. They were created in the nuclear furnaces of stars, and the only way for them to get into your body is if those stars were kind enough to explode…The stars died so that you could be here today.”

I’m comforted by the thought that if we were to ever meet intelligent aliens out there in the universe, the first thing that I would want to convey to these aliens would be our bodies (if these aliens had bodies) could very well be comprised from atoms expelled from the same star over four billion years ago. I would express awe that on the most fundamental level, our atoms are a part of the same cosmos, inanimate and incapable of any sentient thought, but that through evolution, these atoms were arranged in such a way that in this form they had been incorporated into beings not only endowed with reason, compassion, and empathy, but that for the first time in the history of the universe, the cosmos found a way to meditate onto itself and contemplate its own existence.   

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Embryonic Universe

February 6, 2012

Patterns of embryonic development provide important clues to the evolutionary relationships among animals. Animal cells differentiate into tissues during development that contrast with each other based on their function; these tissues are called layers . These patterns Diploblastic animals develop two embryonic cell layers and triploblastic animals develop three. In embryogenesis, the stage of embryo development, three distinct tissue layers form that will grow into organs, called the endoderm, the ectoderm, and the mesoderm. Ectoderm layers develop into nervous tissues, mesoderm layers develop into organs and muscles, and endoderm layers develop into the epithelial tissues that line the body cavity and surround organs.

Animals with radial symmetry, like cnidarians, produce two germ layers called the ectoderm and endoderm making them diploblastic. Some animals with bilateral symmetry produce a third middle layer between these two layers called the mesoderm making them triploblastic. These layers will develop into to all of an animal’s tissues and organs through the process called organogenesis that forms fully-mature organs and organ systems in animals. Diploblastic animals like cnidarians have only the ectoderm and endoderm tissue layers and thus because they lack the mesoderm, creatures like jellyfish don’t have organs. On Earth, triplobastic animals are divided into two categories based on their development. Differences in patterns of early development also characterize two major clades of triploblastic animals, the protostomes and deuterostomes.

A multicellular organism begins its development as an embryo. A series of embryonic stages will create an independent organism. In one of the earliest stages of embryonic development, a zygote will develop into a blastula. The blastula is a hollow sphere of cells formed during the early stages of embryonic development in animals. Gastrulation is another phase in the embryonic development of animals, during which the single-layered blastula is reorganized into a gastrula when the three distinct germ layers form. In the gastrulation of a diploblast some of the ectoderm cells migrate inward forming the endoderm layer. The archenteron is a primitive gut that forms during gastrulation in the developing blastula. A blastopore is an opening into the archenteron during the embryonic stages of an organism. The distinction between protostomes and deuterostomes is based on the direction in which the mouth, or stoma, develops in relation to the blastopore.

On Areios as on Earth, deuterostomes are distinguished by their embryonic development; in deuterostomes, the first opening called the blastopore becomes the anus, while in protostomes it becomes the mouth. In deuterostomes, the original dent becomes the anus while the gut eventually tunnels through to make another opening, which forms the mouth. For protostomes on Areios the dent formed the mouth while the anus was formed later, at the opening made by the other end of the gut. In protostome development, the first opening in development, the blastopore, becomes the animal’s mouth. In deuterostome development, the blastopore becomes the animal’s anus.

Cleavage is the division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. Cleavage ends with the formation of the blastula. Protostomes have what is known as spiral cleavage which is determinate, this meaning that the fate of the cells is determined as they are formed. Each cell produced by early embryonic cleavage does not have the capacity to develop into a complete organism. Deuterostomes have what is known as radial cleavage that is indeterminate; when the original cell in a deuterostome embryo divides, the two resulting cells can be separated, and each one can individually develop into a whole organism.

The genes that control the development of animals are an amazing testament and this is the single greatest piece of evidence to support the idea that all life on Earth shares a common origin. In upcoming posts, we will explore the identical genes common to all animals that regulate development and growth.

This graph outlines the defining characteristics of indeterminate deuterostomes and determinate protostomes.

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.

 

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.

 

Enveloping Unvierse

October 4, 2011

Carl Sagan wrote that if the Earth were the size of a globe our atmosphere at that scale would be about as thin as a single sheet of paper. Yet the air we breathe is so fundamental to life that even the tiniest changes in the composition of our air could cause cascading climate change on a global scale. While carbon dioxide is present in only trace amounts, scientific consensus indicates at a change from 292 parts per million today to 380 parts per million by the next century could spell disaster for human civilization through rising sea levels, changes in established wind and ocean currents, melting ice caps and desertification associated with the overall average trend of global warming. And so atmospheric regulation is essential to the continuing survival of all life; this biogeochemical process is mainly controlled by single-celled organisms.

Our atmosphere on Earth is mostly made of nitrogen, but it’s also about 20% oxygen. Oxygen is a corrosive gas that is dangerous under high concentrations because of how reactive it is with other chemicals. But this concentration of oxygen has been by no means stable over the last four-and-a-half billion years; oxygen levels in our atmosphere have been virtually non-existent until about half a billion years ago, when the so-called Great Oxidiation Event (GOE) took place. The GOE released huge plume of oxygen into the sky over the course of a few million years, radically altering the compostition of life on Earth and giving rise to the ancestors of the eukaryotes. Early life on Earth was anaerobic, meaning that it could function without oxygen. While aerobic animal life takes in oxygen and burns it during metabolism to create carbon dioxide and energy as waste, anaerobic life uses a myriad of metabolic pathways to produce energy, reducing molten iron, acetate, sulfate, hydrogen gas, or other inorganic molecules to produce their energy.

It wasn’t until the rise of cyanobacteria that any appreciable oxygen could be produced. These cyanobacteria are blue-green algae that performed photosynthesis by taking in sunlight, carbon dioxide and water to grow. One byproduct of this reaction was oxygen gas. The early Earth environment was highly reducing, meaning that it would readily absorb any oxygen and quickly oxidize something in the environment. Substrate like iron (III) dissolved in the water would readily oxidize and become iron (II) oxide, which was insoluble in water and would sink to the bottom of primordial seas. We find these banded iron deposits around the world and they are a ready source of the iron we use in modern manufacturing. The presence of banded iron formations would indicate the presence of oxygen being produced by cyanobacteria at the time, so we can reasonable assume that aerobic photosynthesis was going on around 2.1 billion years ago. In fact, cyanobacteria were so pervasive on Earth that their combined exhalations of oxygen radically altered the composition of air.

Areios’s atmosphere is mostly nitrogen, like the Earth’s atmosphere, but the outgassing of volcanoes and the rapid destruction and creation of crust means that oxygen is less abundant in the atmosphere, which has profound implications for the development of animal life. Combine this with the later start for photosynthesis, and this means that aerobic life doesn’t appear until about 12 billion years into Areios’ existence, yet this kind of more complex life persists for over 3 billion years before the surface temperature gets too hot for photosynthesis to maintain itself permanently. Fifteen billion years after creation, the planet’s atmosphere undergoes another profound change. As Hemera gets brighter, the atmosphere would start to slump off and this would alleviate some of the heat that gets trapped in the Areiosan atmosphere. Eventually the atmosphere becomes so thin with carbon dioxide that there isn’t enough CO2 to fuel photosynthesis and plants would die off en-masse. This drop in carbon dioxide would eliminate the greenhouse effect on Areios, and in turn this massive die-off would incite the next ratcheting up of carbon dioxide, which would in turn lead to a positive temperature feedback loop. Oceans would boil over until the last life left on the planet would paradoxically resemble the earliest life; a halophilic thermophile. Eventually, even this hardy creature wouldn’t be able to survive Areios would once again be a world sterile of all life. Temperature would still rise, though, and would boil the carbon dioxide out of the carbonate rocks in the crust, causing a runaway greenhouse effect like the one that we see on Venus. Sadly, this is the fate of all terrestrial planets as their parent star grows old; the same fate awaits our own planet earth in the coming eons.

Long after the Earth's atmosphere boils away, our Sun will evolve into a Red giant star.

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.

Eurytopic Universe

August 2, 2011

Temperatures are on the whole lower on Areios and combined with lower levels of oxygen means that all organisms on Areios are limited by these conditions. The aliens we find on this world are not towering monsters; Areiosans are tiny by comparison to their Terroan cousins. The largest animals on Earth are creatures like sequoias or blue whales, but Areiosans pale in comparison to this. The largest Areiosans are about the size of a horse. Clonal colony organisms like honey mushrooms and coral reefs however, are a different story. On Earth, aspen trees are a conglomerate of root systems that some ecologists argue could be construed as a single organism. Areiosans have much more surface area to sprawl out, more wide open spaces to colonize. The immense gravity keeps them down though. One wouldn’t find anything resembling a giraffe on Areios; most creatures heed gravitropism on Areios, growing outward not upward. Fungi cover huge swaths of Areiosan continents, filling up niches usually afforded to moss or lichens on Earth. And the oceans are just as teeming with life; purple and red algae blanket the surface of oceans, tinting the seas blood-red. These algae colonies are the lifeblood to all animal life because they serve as the organisms on the planet to replenish oxygen by virtue of the dearth of plant life on Areios. Their origin paves the way for animal life to evolve later on.

The first algae don’t appear on Areios until there is enough sunlight penetrating the lower atmosphere to support photosynthesis. The smog of the Areiosan atmosphere blocks most of Hemera’s light from breaking through, but as the star brightens, it begins to overcome the hazy atmosphere and penetrate to the surface of the planet. The first algae descended from aquatic organisms floating on the surface of oceans, eating the iron dissolved in the water. When the faint slivers of ultraviolet light broke through the atmosphere, it would cause die-offs of the surface protists. A mutation in a gene that coded for a membrane protein changed the function of a surface protein, allowing it to transmit and reflect light instead of absorbing it, acting like a sunscreen. Channeling those ultraviolet photons outside of the cell, this novel protein is of benefit to these protists because they no longer risk exposure to dangerous ultraviolet rays. This rudimentary sunscreen is the first step towards building photosynthesis on Areios.

Plants on Earth are fine-tuned to utilize the light coming from the Sun, which means that plants transmit mostly red and yellow light while green light bounces off the pigments and into our eyes, which is why we plants as green. But these colors are only specific to plants on Earth, which are calibrated to maximize the amount of energy they can extract from the light from our Sun. But on another planet, a different Sun would put out a different range of the visible light spectrum more than our Sun and this would mean that plants on those planets would reflect a different color on the spectrum and we could see plants that range from jet-black to silvery-white and any color in between. On Areios, there are no plants because sulfur dioxide withers cellulose and burns the chlorophyll pigments plants use. While algae possess a unique bacterial form of chlorophyll, they are not true plants. The only way to run photosynthesis on Areios is within the insulating environment of the ocean. Photosynthetic algae on Areios have to rely on the dim light from Hemera, so photosynthesis on this planet relies on yellow and green light, so instead algae have a dark blue-violet color to help their pigments absorb light.

Over time, mutations accumulated in this population that led to the appearance of very basic mechanism for electrons to pick up the photons that strike its surface. With successive generations cells evolved more efficient ways to pick up photons and ferry them outside the cell. Somehow in piecemeal additions to the mechanisms of these cells, the photons that once were an occupational hazard for these surface-dwelling protists became a source of fuel for future populations; these photons got gobbled up by electrons and passed like a game of hot-potato through the cell membrane of these protists. Those electrons became a currency for a metaphorical toll booth that allowed protons passage out of the cell. These protons carry a positive charge and there is a charge gradient when you compare the inside of the cell with the outside of cell. But protons would not ordinarily want to move outside of the cell, and so special proteins embedded within the cell have to facilitate the movement of protons outside of the cell. This movement of protons across the cell membrane of a protist is called the proton motive force that fuels ATP synthesis.

On our world, plants appear green, but not this need not be the case; planets orbiting different stars could host different-colored plant life

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

Empyreal Universe

July 5, 2011

ATP synthase is an enzyme embedded at the end of the electron transport chain that creates ATP. Protons from outside the cell pass through the ATP synthase enzyme into the cell. This energy drives the ATP synthase to string phosphates onto a molecule of adenosine and create ATP. Areiosan cells function remarkably in the same way, except ATP synthase strings molecules of arsenate to a molecule of mercapto-adenosine, which is an analogue of adenosine that features sulfur built into the structure. It’s remarkable how analogous our biochemistry is with Areiosan life. Despite a different set of chemicals, the reactions inside our cells seem to mirror those on Areios. Our biochemistry is so analogous that it is reasonably clear to suggest that life adheres to a specific set of chemical pathways and even from one world to another, the same kinds of chemical reactions are preserved, albeit with slight changes in the chemical reagents used.

 
All life uses an electron transport chain to shuttle electrons through their cell membrane, powering pumps to make their fuel source, the molecule called adenosine troposphere (ATP). The electron transport chain for an organisms that can undergo photosynthesis begins when a discrete packet of light called a photon gets passed around through a cell‘s machinery. First of all, light can behave as a particle called a photon. Photons can come in different ‘colors’ that correspond to the wavelength of that photon. The visible light spectrum ranges from blue-violet on one end of the spectrum, and red on the other end of the spectrum. Blue light has the shortest wavelength of visible light while red light has the longest wavelength. Wavelength corresponds with how many times a wave of light cycles from start to finish. Each wave can be thought of a single photon, so blue light has more energy per unit length because a shorter wavelength means more waves per unit length and therefore more energy and photons are available.  

 
Photosynthetic organisms on Earth rely on mainly red and yellow light to power photosynthesis, but this need not be the case. Scientists proffer that plants could use light as far from the lower end of the infrared spectrum to the upper end of the ultraviolet spectrum. The output of the parent star determines the color that a plant will utilize; red and yellow light are the most abundant wavelength of photon emitted from our Sun, so the vast majority of organisms utilize that most abundant source of energy rather than blue or green, which is not as available. But Areios’ star Hemera is characteristically dimmer than our Sun, so it shines with an orange-red glow. For algae on Areios, they tend to absorb more green and yellow and reflect blue and violet light. Because there is no plant life on Areios, redish and purple algae are among the few photosynthesizing organisms on the planet and the ocean surfaces are covered in it, giving much of the world a blood red or violet hue. These algae are amongst the oldest photosynthetic life forms on Areios, and while they cannot undergo photosynthesis or produce oxygen, they play a major role in most ocean ecosystems; because they can tolerate high concentrations of salts in Areios’ briny seas, they are the basis for several aquatic food webs. Some of these purple algae don’t rely on chlorophyll at all, but use a pigment similar to rhodopsin, like the coloring found in human retinas, to absorb light and power their ATP synthesis.
But every photosynthetic creature faces a limitation on how far down the visible spectrum they can utilize. Called the red edge, plants on Earth avoid absorbing light coming from the infrared end of the spectrum because they have to protect themselves from overheating. This isn’t as big of a problem for Areioan life because Areios is on the whole colder than Earth in terms of average temperatures.

Infrared red light is essentially what we perceive as heat and while algae on Areios can absorb infrared light, they too meet a limit on much they tolerate. Their red edge is around infrared wavelengths of 1.5 μm or so, but there are other organisms on Areios that can tolerate much greater into the infrared. Some creatures can see well into the infrared rage enough that their eyesight does not depend on any visible light. Their eyesight would be nearly identical to the infrared telescopes that are used to study astronomical bodies. Perhaps the most astonishing impact of this is that some creatures on Areios would be able to see the universe from a totally different perspective than humans; their infrared vision could view the oldest objects in the universe unaided by a telescope or observatory like we humans must use. Perhaps most amazing of all is that these creatures can do so without the need for cryogenic coolants. Our earth-borne telescopes need to be cooled down to near-absolute temperatures to work in the far infrared spectrum, but Areiosans are not encumbered by that limitation at all. Outside their murky atmosphere lies an exotic universe that they can see with their own eyes. Or eye.

 

This photo of the milky way galaxy shows a different view of our galaxy when viewed in the infrared. This is how our universe looks from view of Areiosan life.

Efficacious Universe

June 26, 2011

The earliest form of photosynthesis on Earth was thought to be the result of a mutated gene that coded for a sunscreen pigment. When the earliest life on Earth spread out from the hydrothermal vents, these organisms eventually spread across the entire ocean and found their way closer to the surface in search of food. However, the surface of the oceans were all but sterilized because the radiation being belched from our rambunctious Sun, which was more dangerous than today’s more placid Sun, would have killed anything that got too much exposure. Some cells adapted to this environment by capitalizing on a novel pigment that could protect the cell’s machinery by absorbing any UV radiation that might strike the cell’s surface. This pigment could transmit visible light away from anything inside the cell that could be damaged and over generations a species found a way to utilize that light to transport electrons through its membrane.

The electron transport chain is a metabolic pathway that creates ATP, the energy source for our cells. Animals use oxidative respiration to replenish a chemical called NADH that fuels the electron transport chain. Other organisms like bacteria use anaerobic respiration to generate NADH, but this isn’t as efficient and it doesn’t produce as much ATP from this older pathway. In either case, the NADH produced from these pathways donates its proton and carries electrons that can be harvested for use in the electron transport chain. These electrons are picked up by an electron carrier molecule that shuttles the electrons across a section of the cell membrane. The price to ferry these electrons through the cell membrane is to push a proton from outside the cytoplasm to inside of the cell membrane. This process of paying protons to move electrons culminates when those electrons get passed across the entire electron transport chain, then those electrons get attached up by an atom like an oxygen or sulfur along with two hydrogen atoms that got pumped inside the cell.

In photosynthesis, a photon that strikes a structure within a cell called a thylakoid gets passed through a pigment like chlorophyll until it reaches the end of the line and dumps that energy onto an electron; like a game of hot-potato that photon gets passed through proteins called antenna systems until it reaches that electron and excites it. Plants and other organisms that undergo photosynthesis have two separate and consecutive photosystems that work in series. Electrons are normally in a so-called ground state, but when they suck up the energy of a photon, it causes them to jump into a higher energy state. That electron flies off of the chlorophyll molecule and gets funneled into the electron transport chain. Photosystem II funnels photons through the thylakoid membrane of a chloroplast to split water apart; this replenishes the electrons lost when that photon carries an excited electron from the pigment molecule chlorophyll through the electron transport chain. This leaves the chlorophyll molecule with a positive charge and in order to reset that molecule back to a more stable form, water molecule gets ripped apart; one of its electrons gets incorporated into the chlorophyll. Photosystem I funnels another photon in to replenish NADH, an electron donor that powers the Calvin cycle that creates sugar for plants. The hydrogen atoms from water float around inside the cell until they get used to pay the ferry that moves electrons across the thylakoid membrane while the oxygen atom gets released into the atmosphere. This is how oxygen got built up in our atmosphere on Earth; the combined photosynthesis of early bacteria and plants belched out so much oxygen into the atmosphere that it poisoned most of the anaerobic life on Earth at the time. More on that later.

Photosynthesis went on before the advent of oxygen in our atmosphere; that and a process called chemosynthesis used a different molecule to accept electrons at the end of the electron transport chain. In these processes, sulfur and hydrogen sulfide are used instead of oxygen and water as the final recipient of electrons channeled through the electron transport chain. A form of anaerobic photosynthesis used by purple and green sulfur bacteria, for instance utilizes the same mechanisms of photosynthesis to create sugars from visible light, but this pathway only requires photosystem I and not II.

This diagram outlines the path an electron takes across the thylakoid membrane to complete the electron transport chain and power ATP synthesis in a cell.