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.   

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.

 

Enduring Universe

June 6, 2011

We encountered this concept of a shadow biosphere that suggests some organisms on Earth may be relics of a previous genesis event. Right now, this is just speculation on the part of some astrobiologists who haven’t been able to find prove of this idea yet. And if life truly did arise on Earth more than once, where is it now? What does it look like and how does it compare to life as we know it now? How would we look for evidence that this actually happened? The most straightforward way to find answers would be to test the genome of bacteria from as many different locations as possible, and the more exotic, the better. (After all, it’s unlikely that something as big as a giraffe for example could have spawned from a different origin event, but something as small and elusive as a bacteria could go unnoticed unless we found it in the backdrop and sequenced its genome.) We would want to look for places that would be cut off from the rest of the biosphere; like miles underground. Scientists found bacteria colonies that consumed hydrogen bubbling from the crust miles below the surface in an abandoned South African mine. DNA analysis showed that this germ was related to all other life on Earth, but what does that mean? How would we know if life were alien to the planet?

If life as we know it didn’t use DNA or RNA, but relied on a different molecule for storing genetic information, then we might see something wildly different from life as we know it. Peptide nucleic acid (PNA) is composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds; the structure is more stable under high temperatures and low pH so it’s possible that it could have been incorporated into early cells and that DNA only came later because DNA is more efficient at replication. Another analogue, threose nucleic acid (TNA) is a polymer used by biochemists in studies on DNA; this analogue can function like DNA or RNA, but TNA is simpler chemically, so it could have been a precursor to RNA.

While the evidence to support a TNA or PNA-dominated biosphere isn’t readily accepted by most molecular biologists, the RNA world hypothesis has enjoyed some support by researchers over the last 30 years. Because RNA can act as an enzyme protein and an information-storing nucleic acid, this versatile chemical is thought to have preceded the advent of DNA, leading some to suspect that early life ran off of RNA and not DNA. It wasn’t until later when a genetic accident could have spawned DNA, which would have dominated the life at the time because it could more efficiently copy itself.

Areiosan life runs off of PNA, but it has a triple helix structure. This idea isn’t new to biology; Linus Pauling suggested DNA might have a triple helix structure back in the 1950’s, but the discovery of DNA’s double helix structure by Watson and Crick completely shattered that idea. Still, when molecular biologists use PNA, it latches itself onto the double helix structure and forms a totally new triple helix that stabilizes DNA under higher temperatures and lower pH. The latter is imperative for Areiosan life because of the prevalence of sulfur in the environment. Sulfur dioxide and trioxide readily form sulfuric and sulfurous acid in contact with water, so increased acid rain has lowered the pH of Areiosan bodies of water. So while the acidified oceans would warp and denature Terroan DNA, Areiosan PNA doesn’t get bent out of shape by higher acidity.

DNA undergoes mutations regularly because the process of transcribing new DNA during cell replication is imperfect. DNA can be miscopied during transcription, but DNA polymerases that add base pairs to DNA during replication can correct some of these errors during a stage called elongation in eukaryotic cells. Because this PNA’s base pairs are harder to pry apart under moderate pH, the proofreading process in Areiosan cells is shorter than in Terroan cells. Because of this, a certain type of error called a mismatch error abounds in Areiosan cells because once replication is complete; there is no proofreading mechanism to follow like with our biology. Despite radically different mechanisms to mitigate mutations to the nucleic acid, both Earth life and Areiosan life experience identical rates of mutation. Mechanisms for repairing DNA are not perfect and these imperfections that allow mutations to occur spur the creation of novel genetic material. If there were no mutations, there would be no evolution and each individual would be a carbon copy of the parent; this would be disastrous because if every individual were exactly vulnerable to the same stresses, then a single event would wipe out an entire population. Mutation causes a varying ability for survival in individuals of a population, and this diversity can provide resilience to a population. Some of those mutations will prove to be deleterious to the individual, but the heritable mutations that don’t manage to wipe the individual tend to persist or even propagate within the population. These errors in DNA replication are the basis for new genetic traits, but if this process is too imprecise, it would kill off too many individuals and prevent that material from ever being propagated. The rate of mutation is therefore fine-tuned to allow “a balance between the evolution of species and the survival and reproductive success of individual organisms.”

This diagram shows the configuration a stable triple helix used on Earth in drugs for cancer treatment.

Emulous Universe

May 4, 2011

DNA is such a fragile molecule that some researchers don’t think it could have survived in the hydrothermal vents outside of a cell membrane where the earliest life was thought to develop. This is an enigma for researchers studying the origin of life. DNA consists of a double helix molecule that resembles a twisted ladder; the backbone of DNA are linked groups of phosphate chemicals These negatively charged strands run antiparallel to each other, meaning that the top of one strand runs parallel to the bottom of the second strand. Areosian life is truly alien because instead of the familiar phosphate, it uses arsenate ions as a backbone. Arsenate is a polyatomic ion with an arsenic atom in the center and four oxygen atoms bonded to the central arsenic. And Areosian DNA gets weirder still because it is a triple helix.

The ends of a DNA molecule are marked as 3’ (three-prime) on one end and 5’ (five-prime) on the other, so our antiparallel strands link a 3’ to a 5’ end and vice versa. This is important because DNA replication proceeds from an area called the origin of replication on both strands in the 5′-to-3′ direction, forming two replication forks where an enzyme called helicase unzips DNA into two strands. RNA resembles a single strand of DNA, but instead of thymine, RNA exclusively uses the base uracil, which binds to adenine.

In the process of RNA replication called transcription. RNA polymerase unzips a DNA molecule by breaking the hydrogen bonds between complimentary nucleotides. RNA nucleotides are paired with complementary DNA bases. RNA sugar-phosphate backbone forms with assistance from RNA polymerase. Hydrogen bonds of the untwisted RNA+DNA helix break, freeing the newly synthesized RNA strand. If the cell has a nucleus, the RNA is further processed in a reaction called methylation and then moves through the small nuclear pores to the cytoplasm.

Some scientists speculate that there was a time when life may have used RNA instead of DNA, but there is little evidence to support it. Some have cited that retroviruses based on RNA could indicate that DNA need not have always been the nucleic acid used by life, and that retroviruses may be a throwback from the time when an RNA-World existed. Retroviruses are viruses that run off of RNA-hardware, and Astrobiologist Peter Ward in his book Life As We Do Not Know It, proffers a title for these earlier life forms as members of his proposed kingdom of Ribosa, or RNA-based life.

DNA on Earth uses the same four nucleic acids. And these four nucleic acids come in two categories; pyramidines and purines. Pyramidines are aromatic hydrocarbons like uracil, cytosine and thymine with nitrogen in the 1,3 position of a six-member ring. Purines are organic compounds like adenine and guanine that consist of a pyrimidine ring fused to an alkaloid imidazole ring. Adenine and thymine pair together with 2 hydrogen bonds just like guanine and cytosine pair together with 3 hydrogen bonds. Areosian life uses entirely different purines and pyramidines, but these chemicals function in much the same way as DNA. For instance, Areiosan life features thiopurines, which incorporate sulfur in a purine’s pyramidine ring. Chemicals like mercaptopurine or tioguanine can be found Areiosan cells. Their pyridimine bases incorporate fluorine in their structure, with fluorouracil, floxouridine and gemcitabine as analogues of the purine bases in our cells. These analogues are called antimetabolites because some chemicals like fluorouracil are so chemically similar to uracil that they interfere with our metabolism. These analogues are used in chemotherapy because they interfere with the function of cancer cells. But in Areiosan cells, they function like the real thing and while they may be different from a chemically perspective, they are not fundamentally different in any other way. The machinery inside their cells works just like the machinery in our cells, but the parts are just made of a different material.

RNA synthesis separates the DNA strands and RNA polymerase builds RNA in the 5' to 3' direction, using one of the DNA strands as a template.