Of Junks and Dark Stuffs – Two Grand Puzzles that Parallel in Scope and Mystery
Our understanding of the human genome, I sense, is more akin to how much we now know about the universe and less of, as we once thought, a straightforward exercise in reading a conventional map. Why? The observable universe (the parts that we can see) makes up to less than 5% of the entire universe. Conversely, the parts that are hidden from us at this time: roughly 68% of the universe is dark energy, and dark matter makes up about 27%. So, the parts - the majority parts – of the universe that we don’t see are more likely the keys in understanding what really make the universe tick.
Dark Energy
Dark energy, perhaps, results from weird behavior on scales smaller than atoms, the physics of quantum mechanics allowing energy and matter to appear out of nothingness (although only for the tiniest instant). The constant brief appearance and disappearance of matter could be giving energy to otherwise empty space. It could be that dark energy creates a new, fundamental force in the universe, something that only starts to show an effect when the universe reaches a certain size. The force might be temporary, causing the universe to accelerate for some billions of years before it weakens and essentially disappears.
Or perhaps the answer lies within another long-standing unsolved problem, how to reconcile the physics of the large with the physics of the very small. Einstein's Theory of General Relativity explains everything from the movements of planets to the physics of black holes, but it simply doesn't seem to apply to the scale of particles that make up atoms. To predict how particles will behave, we need the theory of quantum mechanics, which explains the way particles function, but it simply doesn't apply on any scale larger than an atom. The elusive solution for combining the two theories might yield a natural explanation for dark energy – a tall order.
Dark Matter
Dark matter, unlike normal matter, does not interact with the electromagnetic force. It does not absorb, reflect or emit light, which makes it extremely hard to study. In fact, we only are able to infer the existence of dark matter from the gravitational effect it seems to have on visible matter. One idea is that dark matter could contain "supersymmetric particles" – hypothesized particles that are partners to those already known in the “Standard Model”.
Dark matter candidates arise frequently in theories that suggest physics beyond the Standard Model, such as supersymmetry and extra dimensions. One theory suggests the existence of a “Hidden Valley”, a parallel world made of dark matter having very little in common with matter we know. If one of these theories proved to be true, it could help scientists gain a better understanding of the composition of our universe and, in particular, how galaxies hold together.
The Human Genome
In comparison, the identifiable protein-coding portions – what we traditionally think as the functional parts of a gene – make up only to less than 3% of the whole genome. The remaining parts, the so called “junk”, “non-protein coding”, “selfish DNA”, or, I would name, the “dark DNA” portions make up the majority of the total sequence, 96% plus of the entire genome.
Junk DNA
The term ‘junk DNA’ was introduced in 1972 by Susumu Ohno, as a provisional label for the portions of a genome sequence for which no discernible function had been identified. Today, “junk DNA” is often used in the broad sense of referring to any DNA sequence that does not play a functional role in development, physiology, or some other organism-level capacity. However, recent research studies have identified non-coding DNA sequences that appear to have roles in basic processes such as tissue and organ development, response to hormones, and regulation of gene expression. For example, potential mechanism for non-coding DNA that might increase the risk of heart disease: in mice lacking certain non-coding regions, two genes shows decreased expression, Cdkn2a and Cdkn2b, which affects muscle cells in the aorta - obstructing blood flow to the heart. Most scientists now think that ‘junk DNA’ is actually a massive control panel with millions of switches regulating the activity of our genes.
Epigenetics
Epigenetics involves genetic control by factors other than an individual's DNA sequence. Epigenetic changes can switch genes on or off and determine which proteins are transcribed.
Consider the fact that our cells all have the same DNA, but our bodies contain many different types of cells: neurons, liver cells, pancreatic cells, inflammatory cells, and others. In short, cells, tissues, and organs differ because they have certain sets of genes that are "turned on" or expressed, as well as other sets that are "turned off" or inhibited. Epigenetic silencing is one way to turn genes off, and it can contribute to differential expression. Silencing might also explain, in part, why genetic twins are not phenotypically identical. In addition, epigenetics is important for X-chromosome inactivation in female mammals, which is necessary so that females do not have twice the number of X-chromosome gene products as males. Within cells, there are at least three systems we now know that can act as molecular “switches” in gene expression: DNA methylation, histone modifications, and RNA-associated silencing.
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