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

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.