The dumbest science question ever?

From NASA/Wikimedia commons: The Hubble image shows the paired galaxies very close together with streams of stars being pulled out of the galaxies. The colliding "parent" galaxies lose their shape and smoother galaxies are formed. The whole merging process can take less than a billion years.

I don’t know if this qualifies as the dumbest science-related question ever, but it’s one that’s been bothering me for, oh, years. If you google it, the hits that turn up are, ironically, all religion related, and no help at all.

The question: Why was life such a hit? Rephrased: Why did life, once it got going, persist?

Maybe you know what I mean. Everywhere we look on Earth (almost), we find life. In places where you’d think nothing could evolve, much less survive. There are the bacteria living two miles deep in the Earth, the life flourishing in lava tubes, the organisms that surprised us in such inhospitable places as geothermal vents, Antarctic lakes, and yes, Mono Lake in California.

Why was life such a big hit once Nature got things going? In a more evolutionary context, what benefit do natural processes derive from life? Even after cataclysmic losses in mass extinctions, life bounces back.

Yes, of course, after those extinctions, niches were more readily available than a cheap foreclosure in Las Vegas. And of course, when life first arose, the world was one big niche just waiting to be partitioned. But why are there no boundaries on the blue planet? Hardly anywhere to go where life isn’t?

Like I said, this could be the dumbest science-based question ever asked. I’m assuming some kind of evolutionary context for life itself in the larger backdrop of the physical world, a world that evolves ever so inexorably to a universal heat death that our little minds (or maybe it’s my little mind) can scarcely encompass. Do life and its many processes get us there faster, urge entropy’s expansion? That, of course, assumes some ultimate, seemingly predetermined goal of transformation into heat and an ultimately messy demise.

That assumption may be and probably is a huge misstep. After all, the universe has got some pretty big transformation engines without turning to a teensy little mechanism like life. In other news, it would actually link the second law of thermodynamics and evolution directly, instead of leaving them as fodder for arguing creationist worldviews.

But it feels like a big question. The related question is, Is it a big, stupid question?

Beautifully lifeless: the clearest ocean in the world

Thermohaline circulation

Because of the ability of UV light to shred biological molecules, researchers have speculated that life on Earth may have arisen in some dark corners, possibly under rocks or in the ocean depths where UV waves cannot reach. If that’s the case, we can rest assured that wherever life arose, it couldn’t have been a place containing the “clearest ocean waters on Earth.” That recognition today goes to a patch of water the size of the Mediterranean but lying in the middle of the Pacific, an ocean with a reputation for bounty. This area of the Pacific, however, although boasting waters of a unusual, deep violet color, is as lifeless as it is lovely.

Tough research job, but someone’s gotta do it

Researchers traveling to the area in October 2004 had been attracted to this part of the Pacific—stops included Tahiti, French Polynesia, Easter Island, and Chile—because of satellite images suggesting remarkably low chlorophyll levels in the area. This imaging allows scientists to track chlorophyll abundance in the Earth’s oceans, an important indicator of change on a major scale. When chlorophyll is low, life is scarce.

Indeed, when they traveled to the area, the researchers found some of the clearest ocean waters they had ever seen. According to one scientist on the project, the water was as clear as any of the clearest freshwater anywhere on the planet. He compared it, for example, to the clarity of the water from Lake Vanda, a pristine Antarctic lake lying buried under mountains of ice.

No chlorphyll, little life, but great clarity

But this clarity arises from a lack of chlorophyll and a lack of life. The researchers found that UV could penetrate to extraordinary depths in this area of the Pacific, as deep as 100 meters below the ocean surface. This depth sets a record for UV penetration in ocean waters, and its DNA-destroying properties carry responsibility for the dearth of life in this patch of the Pacific.

The mystery of the organic carbon

The researchers did find some evidence of a food web, however. But the organisms that live there, generally bacterial, must survive in a sort of closed system, constantly recycling the nutrients they need to live, such as nitrogen and phosphorus. Strangely, the team found that this particular part of the ocean was full of dissolved organic carbon, which is of biological origin. How an area so devoid of life could produce so much carbon derived from life remains a mystery. Researchers speculate that the bacteria are so busy addressing their nutrient needs in their limited system that they simply do not get around to degrading the carbon.

Out of the mix

Why would the Pacific harbor this clear, beautiful dead zone? The formation of this odd stretch of sea relies on several factors. The Earth’s oceans are a connected, global system of currents, water running not only at the surface but also at the depths. The thermohaline circulation, also known as the “global conveyor belt,” is one of these currents, driven by changes in the density of water in different parts of the globe. As water warms or becomes more saline, its density changes—warmer water is less dense than cold, and saltier water is more dense. As wind-driven currents move water toward the poles, the water cools and sinks when it gets to the high latitudes. This heavier water then flows back into the ocean basins and eventually wells up again. The oldest waters can take 1600 years to make this trip, but in the meantime, waters mix in the basins, making all of the Earth’s oceans pretty similar as they move their components around the planet.

The clearest ocean water on Earth, however, misses the trip. Its location in the middle of the South Pacific ensures that it doesn’t benefit from global river or ocean circulation. It never cools because it’s in the South Pacific, and thus, the water just stays put, clean and clear and almost completely lifeless.

How the genetic code became degenerate

Our genetic code consists of 64 different combinations of four RNA nucleotides—adenine, guanine, cytosine, and uracil. These four molecules can be arranged in groups of three in 64 different ways; the mathematical representation of this relationship is 4 x 4 x 4 to illustrate the number of possible combinations.

Shorthand for the language of proteins

This code is cellular shorthand for the language of proteins. A group of three nucleotides—called a codon—is a code word for an amino acid. A protein is, at its simplest level, a string of amino acids, which are its building blocks. So a string of codons provides the language that the cell can “read” to build a protein. When the code is copied from the DNA, the process is called transcription, and the resulting string of nucleotides is messenger RNA. This messenger takes the code from the nucleus to the cytoplasm in eukaryotes, where it is decoded in a process called translation. During translation, the code is “read,” and amino acids assembled in the sequence the code indicates.

The puzzling degeneracy of genetics

So given that there are 64 possible triplet combinations for these codons, you might think that there are 64 amino acids, one per codon. But that’s not the case. Instead, our code is “degenerate;” in some cases, more than one triplet of nucleotides provides a code word for an amino acid. Thus, these redundant codons are all synonyms for the same protein building block. For example, six different codons indicate the amino acid leucine: UUA, UUG, CUA, CUG, CUC, and CUU. When any one of these codons turns up in the message, the cellular protein-building machinery inserts a leucine into the growing amino acid chain.

This degeneracy of the genetic code has puzzled biologists since the code was cracked. Why would Nature produce redundancies like this? One suggestion is that Nature did not use a triplet code originally, but a doublet code. Francis Crick, of double-helix fame, posited that a two-letter code probably preceded the three-letter code. But he did not devise a theory to explain how Nature made the universal shift from two to three letters.

A two-letter code?

There are some intriguing bits of evidence for a two-letter code. One of the players in translation is transfer RNA (tRNA), a special sequence of nucleotides that carries triplet codes complementary to those in the messenger RNA. In addition to this complementary triplet, called an anticodon, each tRNA also carries a single amino acid that matches the codon it complements. Thus, when a codon for leucine—UUA for example—is “read” during translation, a tRNA with the anticodon AAU will donate the leucine it carries to the growing amino acid chain.

Aminoacyl tRNA synthetases are enzymes that link an amino acid with the appropriate tRNA anticodon.  Each type of tRNA has its specific synthetase, and some of these synthetases use only the first two nucleotide bases of the anticodon to decide which amino acid to attach. If you look at the code words for leucine, for example, you’ll see that all four begin with “CU.” The only difference among these four is the third position in the codon—A, U, G, or C. Thus, these synthetases need to rely only on the doublets to be correct.

Math and doublets

Scientists at Harvard believe that they have solved the evolutionary mystery of how the triplet form arose from the doublet. They suggest that the doublet code was actually read in groups of three doublets, but with only the first two “prefix” or last two “suffix” pairs actually being read. Using mathematical modeling, these researchers have shown that all but two amino acids can be coded for using two, four, or six doublet codons.

Too hot in the early Earth kitchen for some

The two exceptions are glutamine and asparagine, which at high temperatures break down into the amino acids glutamic acid and aspartic acid. The inability of glutamine and asparagine to retain structure in hot environments suggests that the in the early days of life on Earth when doublet codes were in use, the primordial soup must have been too hot for stable synthesis of heat-intolerant, triplet-coded amino acids like glutamine and asparagine.

Why is the sky blue? Blame rocks

Early Earth’s changing landscape…and skyscape

If you traveled back in time to about 2.5 billion years ago, you wouldn’t recognize much of what you saw. The dawning, living planet back in the day sported skies of orange, shaded by an unbreathable atmosphere awash in methane gas. But through the long Proterozoic Era, those skies changed from orange to blue. Usually, we give our thanks for this change to oxygen, but a recent review traces the original actor in the color change drama to rocks. Specifically, to the phosphorus in the rocks.

Phosphorus? Really?

Phosphorus is one of the critical of elements of life. It’s a primary component of a DNA or RNA building block (nucleotide = sugar, phosphate, base). It also happens to be the primary component of the “energy currency” of cells, ATP, or adenosine triphosphate, which is really a nucleotide with three phosphates on it. Many organisms use ATP, and all organisms use phosphorus in their genetic code and their RNA.

And, a major source of it is rocks. So, yes. Phosphorus, really. Read on.

Geochemical cycles and a whole lot of gas

Several independent lines of evidence have shown that oxygen levels rose in two lengthy bursts coincident with bursts of life on Earth. The first gassy increase happened between 2.5 to 2 billion years ago. Fittingly, scientists refer to this rise in atomspheric oxygen as the Great Oxidation Event. One of the effects of the increased oxygen is that rust started showing up in the geologic record. During this Great Event, the single-celled organisms that had thrived under a presumably orange sky grew larger, and mitochondria may have arisen as a result of endosymbiosis. These cellular powerhouses are, in fact, responsible for completing energy extraction from organic molecules and using the energy to build…ATP.

The second big burst of oxygen happened about 1 billion to 540 million years ago, this time coincident with the rise of multicellular organisms and culminating in the blast of diversificiation known as the Cambrian Explosion.

What does oxygen have to do with phosphorus?

The two often hang out together as phosphate, but the real connection here is about phosphate’s contribution to life’s explosions. It may be that geologic processes, such as erosion, caused a gradual but abundant release of phosphorus from rock into the Earth’s seas. With this influx of a key component for building life, the phosphorus facilitated the early Earth equivalent of enormous algal blooms.

And guess what those algae did…and still do? Photosynthesisis. And one of the main byproducts they release from all that busy light capturing and sugar building is…oxygen. That’s the phosphorus-oxygen connection.

So, if a child ever asks you why the sky is blue and you just can’t think of the answer, you can distract them by asking them, “Did you know that the sky used to be orange?”

For your consideration

Double-membrane organelles like mitochondria are thought to have arisen through a process called endosymbiosis. What is endosymbiosis, and how could it have led to the presence of organelles like mitochondria in cells?

The algal blooms described in this paper were enormous and their influence may literally have changed the color of the sky back in the day, but the oxygen buildup and phosphorus release happened over long stretches of geological time. Today, we experience algal blooms, too. Can you identify the causes of these blooms? How do these blooms affect today’s life on Earth? Do the effects seem to be beneficial or adverse?

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