Envisionary Universe

April 2, 2012

Most animals share a set of derived traits not found in other groups of organisms. These traits make animals unique out of every other organism on the planet.  One such trait is specialization.  In specialization, cells start out as un undetermined or undifferentiated lump and “grow up” into different types of cells, like skin cells, bone cells, blood cells and nerve cells.   However, some animals like sponges lack specialized cells.  Advanced multicellular animals have specialized tissues that perform unique functions.   Jellyfish, for example (though they are not in the strictest sense “fish”) have specialized stinging cells called cnidocytes that release a deadly poison when other organisms get too close.   The process of specialization requires a highly-specific set of genes to regulate an animal’s growth and development.  Scientists on Earth have discovered that all animals on Earth share this same set of genes, from organisms as simple as tapeworms to incredibly large and complicated organisms like the blue whale.

This development of animals is controlled by the so-called Hox genes.  These Hox genes are responsible for assigning a location and identity to our cells in order to build body parts.  Hox genes contain within them a DNA sequence known as the homeobox. The homeobox is a DNA sequence found in Hox genes and other genes that code for transcription factors, which is are proteins that bind to specific DNA sequences in order to activate the transcription of DNA into mRNA.  The sequence of amino acids encoded by the homeobox is called the homeodomain.  Our so-called Hox genes are a shared set of programs that determine how all complex animals develop. These genes are so important to the development of all complex animals that just about any mutation in this set of instructions is all but assured to result in the death of the organism.  This means that there are only a few highly specific ways that these genes could be rearranged without killing the organisms during development.  One example of researchers messing with Hox genes resulted with antennapedia, a fruit fly with legs on its head where its antennas ought to be.  It provides evidence that evolution is a ongoing process and that natural selection can explain the evolution of all life on Earth.  If there is a mutation in the hox genes, it would likely cause a deleterious effect (like building a human with feet where their ears ought to be), and that is the reason why organisms seem to be intelligently designed when in reality they are not.  Anything less-than-perfect design that comes by natural selection would get weeded out quickly, leaving only the most exquisitely-designed forms still around. Because of this, virtually every animal on Earth shares the same gene sequence responsible for development. Such genes are astoundingly preserved, maintaining the exact same sequence universally across all deuterostomes over half a billion years of evolution.

This is the single greatest piece of evidence that supports the idea that all animal life on Earth is related through evolution by natural selection.  Only random mutation can explain why our Hox genes work just like the set found in every other animal on Earth. And only hox genes can explain why humans develop gills and a tail as a pharyngula just as fish do.  During our development, however, the hox genes eventually eliminate the gills and tail.  Why would an intelligent designer start to create developing humans as though we were a developing fish, only to remove those fish characteristics anyway later on in development?  The only reasonable explanation is that the genes that are responsible for creating all vertebrates during development were preserved  by natural selection and that these genes are so fundamental to the success of an individual that we’ve relied on the same set of Hox genes, essentially unchanged since the first vertebrates flopped around in the sea.

The Hox genes that all animal life share on Earth reminds me of something poignant that I learned in biology class as a freshman in college.  We are connected in an unbroken lineage to the very earliest lifeforms on Earth.  All life shares a last universal common ancestor and it is by the virtue of our ancestors’ integrity that we all can be alive today.  And I mean not just our human ancestors, either, but our primate ancestors, our mammalian ancestors, and even our chordate ancestors from 350 million years ago.  I marvel sometimes at this fact that on a planet that is over four billion years old, I am alive for at best 100 years, roughly 1-forty-millionth of the history of the planet.  And that the human race being around for at most two million years has only been around one-two-thousandth of the history of the planet Earth.  Any yet my ancestors carried on in an unbroken chain of creation for over four billion years before I came along.  It makes me feel a sense of awe in a way that no religion ever has been able to instill upon me.  I am part of a much larger and much older biological community almost as old as the planet itself.

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.   

Eukaryotic Universe

January 2, 2012

Animals are complex multicelullar eukaryotic organisms. The key word here is complex. There are multicellular prokaryotic organisms like the pond scum Volvox, but what distinguishes plants, animals, and fungi from the protista is the level of organization. Unlike single-celled oranism, animals have body plans. A body plan is the blueprint for the way the body of an organism is laid out. Animal body plans describe the symmetry, body cavity structure, segmentation, and appendages that each animal has. There are two major ways that an animal’s body plan can exhibit symmetry; radial and bilateral. Some organisms like sponges, however, lack symmetry of any kind, but other creatures like sea stars, sea anemones, and jellyfish exhibit radial symmetry. Animal plans that exhibit radial symmetry have no left or right sides.
    Animals body plans that exhibit bilateral symmetry have identical left and right symmetrical halves. Most animals with radial symmetry move slowly or not at all, while animals with bilateral symmetry are able to move more rapidly. Many bilaterally symmetrical animals are cephalized, with sensory and nervous tissues in the head. Cephalization is a trend where bilaterally symmetric animal genera tend to exhibit a distinct anterior head that directs the body.  Bilateral symmetry permits streamlining, favors the formation of a central nerve center, and promotes actively moving organisms. Bilateral symmetry is an aspect of both chordates and vertebrates like fish, amphibians, reptiles, birds, and mammals.
    Early animals did not have an enclosed body cavity. These creatures like flatworms are called acoelomate. Their gut is surrounded by a layer of mesenchyme, which is a loose connective tissue that attaches the gut to a layer of muscle. Roundworms are called pseudocoelomates because they have a fluid-filled body cavity called called a pseudocoelom. The pseudocoelom is lined with a layer of cells called a mesoderm, with the internal organs supported only by the hydrostatic pressure of the fluid within the pseudocoelom. The most complex body cavity arrangement belong to the coelomates. Coelomates have a true coelom, a body cavity surrounded entirely by a layer of mesoderm cells called the peritoneum. The internal organs of coelomates are also surrounded by a layer of peritoneum. This layer of connective tissue can act as a shock absorber against the assaults from the outside world and provides additional stability as a hydrostatic skeleton. A hydrostatic skeleton provides support because the liquid in the coelom can’t be compressed, and the volume and shape of the organism remains constant due to hydrostatic pressure.
    Some organisms exhibit segmentation of body parts; segmentation is the repetition of similarly-sized-and-shaped body parts, usually in a series. Segmentation improves control of movement, especially if the animal also has multiple appendages. This is where Areiosan life differs from Terroan life; on Earth most organisms have an even number of appendages; insects have six legs, arachnids have eight legs, and most amphibians, reptiles, and mammals are four-legged tetrapods. Due to a curious evolutionary quirk in the genes that code for the development of all animals on Areios, Areiosan creatures have an odd number of limbs. On this world, one would find almost exclusively seven-legged bugs and five-legged quintapod reptiles. The genetics of how organisms develop is important to understanding evolutionary  biology and the history of animal life.

On Areios seven-limbed echinoderms like this sea star are commonplace.