Viroids

Viroids

In the laboratory at Cornell University the scientists work on, among other things, prebiological organic chemistry, making some notes of the music of life. They mix together and spark the gases of the primitive Earth: hydrogen, water, ammonia, methane, hydrogen sulphide – all present, incidentally, on the planet Jupiter today and throughout the Cosmos. The sparks correspond to lighting – also present on the ancient Earth and on modern Jupiter.

The reaction vessel is initially transparent: the precursor gases are entirely invisible. But after ten minutes of sparking, we see a strange brown pigment slowly streaking the sides of the vessel. The interior gradually becomes opaque, covered with a thick brown tar. If we had used ultraviolet light – simulating the early Sun – the results would have been more or less the same. The tar is an extremely rich collection of complex organic molecules, including the constituent parts of proteins and nucleic acids. The stuff of life, it turns out, can be very easily made.

Life is certainly more than the amino acids and the nucleotides. Image: © Elena

Such experiments were first performed in the early 1950’s by Stanely Miller, then a graduate student of the chemist Harold Urey. Urey had argued compellingly that the early atmosphere of the Earth was hydrogen-rich, as is most of the Cosmos; that the hydrogen has since trickled away to space from Earth, but not from massive Jupiter; and that the origin of life occurred before the hydrogen was lost. After Urey suggested that such gases be sparked, someone asked his what he expected to make in such an experiment. Urey replied, “Beilstein”. Beilstein is the massive German compendium in 28 volumes, listing all the organic molecules known to chemists and mentioned in one’s of Isaac Asimov’s amazing stories.

Using only the most abundant gases that were present on the early Earth and almost any energy source that breaks chemical bonds, we can produce the essential building blocks of life. But in our vessel are only the notes of the music of life – not the music itself.

Viroids are composed exclusively of nucleic acid, unlike the viruses, which also have a protein coat. They are no more than a single strand of RNA with either a linear or a closed circular geometry. Viroids can be small and still thrive because they are thoroughgoing, unremitting parasites. Like viruses, they simply take over the molecular machinery of a much larger, well-functioning cell and change a from a factory for making more cells into a factory for making more viroids.

Cambrian Explosion and Our Ancestors

Cambrian Explosion and Our Ancestors

Before the Cambrian explosion species seem to have succeeded one another rather slowly. In part this may be because the richness of our information declines rapidly the farther into the past we peer; in the early history of our planet, few organisms had hard parts and soft beings leave few fossil remains. But in part the sluggish rate of appearance of dramatically new forms before the Cambrian explosion is real; the painstaking evolution of cell structure and biochemistry is not immediately reflected on the external forms revealed by the fossil record.

Soon after the Cambrian explosion, the oceans teemed with many different forms of life. By 500 million years ago there were vast herds of trilobites, beautifully constructed animals, a little like large insects. Some hunted in packs on the ocean floor. They stored crystals in their eyes to detect polarizes light. But there are no trilobites today; there have been none for 200 million years. The Earth used to be inhabited by plants and animals of which there is today no living trace. And of course every species now on the planet once did not exist. There is no hint it the old rocks of animals like us. Species appear, abide more or less briefly and the flicker out.

There is always hope. Illustration by Elena

After the Cambrian explosion, exquisite new adaptations followed one another with comparatively breathtaking speed. In rapid succession, the first fish and the first vertebrates appeared; plants, previously restricted to the oceans, began the colonisation of the land; the first insect evolved, and its descendants became the pioneers in the colonisation of the land by animals; winged insects arose together with the amphibians, creatures something like the lungfish, able to survive both on land and in the water; the first trees and the first reptiles appeared; the dinosaurs evolved; the mammals emerged, and then the first birds; the first flowers appeared; the dinosaurs became extinct; the earliest cetaceans, ancestors to the dolphins and whales, arose and in the same period the primates – the ancestors of the monkeys, the apes and the humans.

Less than ten million years ago, the first creatures who closely resembled human beings, evolved, accompanied by a spectacular increase in brain size. And then, only a few million years ago, the first true humans emerged.

Plunging into the Nucleus of the Cell

Plunging into the Nucleus of the Cell

If we plunged through a pore into the nucleus of the cell, we would find something that resembles an explosion in a spaghetti factory – a disorderly multitude of coils and strands, which are the two kinds of nucleic acids: DNA. Which knows what to do, and RNA, which conveys the instructions issued by DNA to the rest of the cell. These are the best that four billions years of evolution could produce, containing the full complement of information on how to make a cell, a tree or a human work. The amount of information in human DNA, if written out in ordinary language, would occupy a hundred thick volumes. What is more, the DNA molecules know how to make, with only very exceptions, identical copies of themselves. The know extraordinary much.

DNA is a double helix, the two intertwined strands resembling a “spiral” staircase. It is the sequence or ordering of the nucleotides along either of the constituent strands that is the language of life. During reproduction, the helices separate, assisted by a special unwinding protein, each synthesizing an identical copy of the other from nucleotide building blocks floating about nearby in the viscous liquid of the cell nucleus. Once the unwinding is underway, a remarkable enzyme called DNA polymerase helps ensure that the copying works almost perfectly. If a mistake out and replace the wrong nucleotide by the right one. These enzymes are a molecular machine with awesome powers.

The enzymes are a molecular machine with awesome powers. Illustration: Elena

In addition to making accurate copies of itself – which is what heredity is about nuclear DNA directs the activities of the cell – which is what metabolism is about – by synthesizing another nucleic acid called messenger RNA, each of which passes to the extra-nuclear provinces and there controls the construction, at the right time, in the place, of one enzyme. When all is done, a single enzyme molecule has been produced, which then goes about ordering one particular aspect of the chemistry of the cell.

Human DNA is a ladder a billion nucleotides long. Most possible combinations of nucleotides are nonsense: they would cause the synthesis of proteins that perform no useful function. Only an extremely limited number of nucleic acid molecules are any good for lifeforms as complicated as we. Even so, the number of useful ways of putting nucleic acids together is stupefyingly large – probably far greater than the total number of electrons and protons in the universe. Accordingly, the number of possible individual human beings is vastly greater than the number that have ever lived: the untapped potential of the human species is immense.

The Living Cells

The Living Cells

The living cell is a regime as complex, and beautiful as the realm of the galaxies and the stars. The elaborate machinery of the cell has been painstakingly evolved over four billion years. Fragments of food are transmogrified into cellular machinery. Today’s white blood cell is yesterday’s creamed spinach. How does the cell do it? Inside is a labyrinthine and subtle architecture that maintains its own structure, transforms molecules, stores energy and prepares for self-replication.

If we could enter a cell, many of the molecular specks we would see, would be protein molecules, some in frenzied activity, others merely waiting.

The most important proteins are enzymes, molecules that control the cell’s chemical reactions. Enzymes are like assembly-like workers, each specializing in a particular molecular job: Step 4 in the construction of the nucleotide guanosine phosphate, say, or Step 11 in the dismantling of a molecule of sugar to extract energy, the currency that pays for getting the other cellular jobs done. But the enzymes do not run the show. They receive their instructions – and are in fact themselves constructed – on orders sent from those in charge. The boss molecules are the nucleic acids. They live sequestered in a forbidden city in the deep interior, in the nucleus of the cell.

An oak tree and I are made of the same stuff. If we go far enough back, we have a common ancestor. Image: © Elena

Human beings grew up in forests; we have a natural affinity for them. How lovely a tree is, straining toward the sky. Its leaves harvest sunlight to photosynthesize, so trees compete by shadowing their neighbors. If you look closely you can often see two trees pushing and shoving with languid grace. Trees are great and beautiful machines, powered by sunlight, taking in water from the ground and carbon dioxide from the air, converting these materials into food for their use and ours. The plant uses the carbohydrates it makes as an energy source to go about its planty business. And we animals, who are ultimately parasites on the plants, steal the carbohydrates so we can go about our business. In eating the plants we combine the carbohydrates with oxygen dissolved in our blood because of our penchant for breathing air, and so extract the energy that makes us go. In the process we exhale carbon dioxide, which the plants then recycle to make more carbohydrates. What a marvelous cooperative arrangement – plants and animals each inhaling the other’s exhalations, a kind of planet-wide mutual month-to-stoma resuscitation, the entire cycle powered by a star 150 million kilometers away.

There are tens of billions of known kinds of organic molecules. Yet only about fifty of them are used for the essential activities of life. The same patterns are employed over and over again, conservatively, ingeniously for different functions. And at the very heart of life on Earth – the proteins that control cell chemistry, and the nucleic acids that carry the hereditary instructions – we find these molecules to be essentially identical in all the plants and animals.

Possibility of Life Elsewhere

Possibility of Life Elsewhere

All my life I have wondered about the possibility of life elsewhere. What would it be like? Of what would it be made? Are the inhabitants of other planets very different from us?

There was once a time before life, when the Earth was barren and utterly desolate. Our world is now overflowing with life. How did it come about?

Probably, all the organic beings which have ever lived on this Earth, have descended from one primordial form, into which life was first breathed. There is grandeur in this view of life… that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been and are being evolved. (Charles Darwin, the Origin of Species, 1859).

Indeed, all living things on our planet are constructed of organic molecules – cosmic microscopic architectures in which the carbon atom plays a central role. But how, in the absence of life, were carbon-based organic molecules made? How did the first living things arise? How did life evolve to produce beings as elaborate and complex as we, able to explore the mystery of our own origins?

In our obsession with antagonisms of the moment, we often forget how much unites all the members of humanity. Perhaps we need some outside, universal threat to make us recognize this common bond. I occasionally think, how quickly our differences worldwide would vanish if we were facing an alien threat from outside this world. President Ronald Reagan, United Nations General Assembly, 21 September 1987. Illustration : Elena