How Did Life Begin-On Earth and Elsewhere?

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Message 2038992 - Posted: 19 Mar 2020, 22:29:16 UTC

Few topics are as central to those interested in SETI than the origins of life. Like other key questions in SETI (how many other intelligent civilizations exist, how long do they survive, do smart machines ultimately replace smart biological life forms, to name a few), scientists would love to provide answers. Yet, in principle, we may never know the one correct solution. For most of human history, the subject was the purview of theologians and myth makers. Nearly every society and sect has featured its own creation myth, for how could thinking beings avoid facing the question? The answer often took the form of: “the gods did it, and this is how.” Aristotle took a naturalistic crack at an answer, and Charles Darwin offered one of the first scenarios based on modern science. The subject of biogenesis is now pursued in chemistry and biology labs, by explorers of far flung environments on the surface of the Earth and beneath its seas, and by physicists applying the rules of thermodynamics. The recent discoveries of hundreds of exoplanets have invigorated interest in the ways in which inorganic molecules assemble into living organisms.

The Greek philosophers proposed that living forms arose spontaneously from “decaying matter” and the like. Flies arose from putrefying matter, aphids from dew on leaves, mice from dirty hay, and so on. These beliefs remained popular well into the nineteenth century. Controlled scientific experiments then showed, for example, that maggots don’t appear on decaying meat when flies were prevented from laying eggs. Louis Pasteur demonstrated that bacteria and fungi don’t arise in sterile media that are properly enclosed. At the time, this supported the popular concept of “vitalism”: that living forms contain a special spark that sets them apart from inanimate objects. Most scientists now view biogenesis as a natural process. They explore the ways in which the conditions of early Earth could have advanced available compounds to more complex chemistry and the beginnings of life. Darwin speculated that life could have begun in a “warm little pond” containing a broth of chemicals and empowered by heat and lightning. Given numerous fits and starts, the seminal process of natural selection eventually kicked in. Natural selection is so “natural” that it seems inevitable: The living entities, and even the first stable assemblies of pre-biotic chemicals, that are better than their neighbors at surviving and producing more offspring will win out. The losers can serve as food for the winners.

A landmark experiment was conducted in 1952 by doctoral student Stanley Miller and his adviser Leslie Orgel. They seeded flasks with features thought to mimic the conditions of early Earth: water, hydrogen, ammonia, methane and a series of electrical sparks to simulate lightning strikes. After a few days, the watery solution became red and turbid. From this simple beginning were formed a number of more complex organic molecules, including two amino acids, the building blocks of proteins (more modern analytical techniques detected nearly a dozen different amino acids in this goo). The modern science of biogenesis had truly begun. Since then, astronomers have upped the ante by detecting many organic molecules-basic building blocks of life-in outer space: in circum-stellar envelopes, in clouds of interstellar gas and dust, in comets and in meteorites that fall to Earth. Noble winning biologist Christian de Duve observed that “the chemical germs of life are banal products of space chemistry.”

But how did life arise from these ingredients? Theories fall into several categories of what came first: metabolism or replication? Metabolism refers to the ability to harness energy from the surroundings to live. Replication, obviously, is the ability to persist and create self-similar descendants. Both likely had to arise early and nearly simultaneously on the pathway to living organisms. Also necessary near the outset was the advent of a “container” to keep the vital contents from floating away. Hence, the precursor of a modern cell. And where did life originate? Was it in Darwin’s warm little pond, in hydrothermal vents deep in the ocean or hot volcanic springs on the surface, in liquid or on the surface of clay-like rocks which can catalyze chemical reactions?


Photo by Matthias Kabel, CC BY 2.5

“Cell first”, or at least “cell early”, scenarios posit that fatty compounds which can spontaneously form layers and droplets were required to sequester local ingredients. Those assemblies which by chance contained chemical groups that form rather easily, are particularly stable, and interact favorably with fatty membranes gained ground and become “proto-cells” which could enlarge, pinch off into daughter proto-cells and begin a pre-Darwinian selection leading to ever more efficient “living cells.” But what constituted the innards of these precursors of life? Current biology may constrain and inspire the inquiries, while remaining cognizant that primitive life differed from present life to an extent we can never fully know. The guts of present Earth biology are proteins which are composed of strings of 20 different amino acids joined by a chemically distinct peptide bond. Proteins serve as catalysts to vastly speed up chemical reactions and build the structures of cells and organisms. Likely their forbearers were much shorter chains of amino acids. Some, on their own or associated with others, may have functioned a bit better than the rest and remained relatively stable, perhaps in growing aggregates that could break apart and grow anew. Countless tries could have provided a wedge towards a precursor of a living cell.

Of course, living cells must not only function, but must also reproduce. Up until the mid-twentieth century, biologists thought that proteins were the bearers of both function and hereditary instructions. That turned out to be wrong. The genetic code for life on Earth is contained in the chains of DNA and RNA, not proteins. (If you know about prions, there are exceptions to the rule.) The chains of DNA and its close chemical relative RNA are made of 4 different nucleotide “bases” which have two key features. They can serve as letters of a genetic code, and each base can bind to a single complementary base to allow for copying of the original sequence after two rounds, and to recognize unique adapter RNA molecules (tRNA) that serve to link amino acids into growing protein chains. (School children now learn that two DNA strands entwine in a double helix, that genes comprise a portion of this DNA “chromosome”, that the coding sequence of a DNA gene is copied into the intermediate strand of messenger RNA, and that message is finally translated via a three-base code into amino acids that are stitched together to form proteins.) This is the language of the recipe book for inheritance that Darwin would have loved to know during his lifetime. But there is a potential stumbling block. In today’s cells, the copying of the DNA and RNA chains, and the assembly of proteins they encode, require a panoply of existing proteins to catalyze the reactions. So, which came first, the chicken of protein enzymes or the egg of DNA?

A possible solution came from the Nobel Prize-winning research of Thomas Cech and Jack Szostak in the 1980s. They independently discovered that RNA strands themselves could fold into shapes that can serve as functioning enzymes. Some of these “ribozymes” could copy and modify RNA strands. The egg and the chicken could be one. Walter Gilbert coined the term “RNA world” to describe an early form of life which was based on both the catalytic and hereditary properties of RNA. The emergance of separate proteins and coding molecules could come later. The first RNA “proto-genes” and “proto-enzymes” to arise by chance would be smaller and less efficient than they are today; eventually to grow and combine to sizes more typical of present life. The advent of protein and gene sequencing revealed a surprising way in which evolution has been speeded up since the first living forms: proteins and genes come in related families. Most protein sequences have recognizable relatives in whole or in part. Duplicated genes are an ancient phenomenon. The extra copies can accumulate mutations, and evolution can “experiment without risk” with variants of a gene until one becomes useful to the organism. Not only that, many proteins are comprised of distinct domains with characteristic properties-such as binding to a particular substance or catalyzing a certain reaction- that are shared in different arrangements in other proteins. The genes that encode these proteins are often divided into the same domains which can be copied and shuffled about the chromosomes. The realization that genes and proteins can arise from duplication and sequence drift, and can be made from combinations of pre-existing modules, has shown an added efficiency in the process of evolution by natural selection. Every functional protein need not be assembled from scratch.

Of course, a primitive RNA world, if there was one, was eventually replaced by the subsequent separation of the instruction and inheritance component of cells (DNA and RNA) from their structural and catalytic products (proteins and the complex carbohydrates and lipids whose assembly they catalyze.) The coding material could become sequestered and increase its stability and fidelity. It could combine and reorganize segments to increase its coding repertoires and integrate expression of functionally related genes, allow modulation of the timing and quantity of gene products, become linked to cell division in an orderly process, and more. All the while proteins were freed to take on different sequences, configurations, cellular locations and multi-element complexes without affecting the structure and enzymatic activity of the genetic coding molecules themselves.

It is obviously possible that life began in very different ways than an RNA world. Many distinctive chemical reactions, starting points and histories have been proposed and are the active subjects of laboratory testing. It would take up far more pages to give them a proper treatment in this limited summary. Though no laboratory has yet made “life from scratch”, scientists have come a long way from looking for maggots to spontaneously arise from rotting meat.

Biogenesis by these natural steps without miraculous intervention has been criticized on several grounds. One objection is that forming life from inanimate chemicals violates the second law of thermodynamics; that entropy cannot decrease. Not so, declare physicists from Boltzman, Schrodinger, Prigogine, to the present theorist Jeremy England who have advanced theories of non-equilibrium thermodynamics which are consistent with a physical drive towards life. Briefly, low entropy sources of energy including sunlight can be converted by molecules into organized forms which “dissipate” such energy into heat. This preserves the global increase of entropy while favoring low entropy compounds and assemblages in a local space, such as a lipid bound proto-cell. Another criticism is the very unlikelihood of arriving at the features of living organisms by chance. But natural selection does not proceed by huge jumps in structure and function. Each variation need only offer a slight improvement in function and survival of itself and its descendants (though not to dismiss the occasional occurrence of a mega-improvement). Biologist Richard Dawkins called this process climbing Mount Improbable by small steps. Some of the most noted critics of Darwinism miss this point. As one infamous example raised by creationists, a magnificently functioning eye could not evolve from scratch in one unfathomable step. It did not have to. Quite likely there occurred numerous modifications of genes and proteins that gave cells light sensing capabilities that allowed their hosts to seek better exposure to sunlight, followed by mutations that improved sensitivity and directionality, and many ensuing steps to arrive at organs which sharply focus images like human eyes. It is telling that biologists have now shown that acute vision has evolved independently several times to produce the utterly distinct eyes of humans, flies, flatworms, octopi and clams. And many living creatures still possess only the cruder light detection systems. As to the timing and the probabilities of life’s beginning, we can only say with certainty that it happened at least once and had tens to hundreds of million years to occur, from the time the infant Earth formed a cool, stable surface to the appearance of single cell organisms apparent in the fossil record. As an alternative, some have championed an idea called “panspermia,” that life arrived on Earth from a previous home in or beyond our Solar System.

There is likely to never be a convincing proof that any scenario must have been the way life arose on Earth, let alone elsewhere in the universe. The best we may hope for is one
(or more) compelling story that is consistent with all of the evidence. Indeed, life may have arisen and died out numerous times on Earth, only to continue into the present with a winning recipe in the “survival of the fittest”, which notably includes elements of chance as well as necessity. As an aside, I wish to mention a salient point made by Richard Dawkins. He claimed that is a common misuse of terms to call the genetic process a “blueprint of life.” That would better describe the outdated notion that germ cells contain a homunculus, a miniature version of the adult to be. The more appropriate term for the genetic code is a “recipe”. It is not a blueprint or an image. The string of nucleotides in the strands of DNA and RNA spell out the way to assemble proteins and the subsequent finished product of a living organism. It is the goal of biogenesis to derive viable pathways from lifeless chemicals to stable entities which contain such recipes.

I’ve left to the end of this far-too-brief discussion of a huge topic, two questions that might belong at the start of this essay: What can we expect of life elsewhere in the universe; and what indeed is “life?” As to the first question, we can all guess. As discussed in an earlier essay in this series (The Drake Equation), astronomers in the last decade have discovered so many planets orbiting other suns that they now believe that planetary systems are a common outcome of the formation of stars from contracting discs of gas and dust. Planets likely outnumber the total of approximately 300 billion stars in our Milky Way Galaxy. Multiple factors constrain the odds of a planet developing life, but many reasonable thinkers contend that the universe is teeming with life forms. Odds are that many different chemical scenarios played out in the environments of other planets, and life began and evolved in ways that markedly differ from the history of Earth. Many inhabited exoplanets could only harbor microbial life. But those that have evolved highly intelligent species could have had billions of years head start on us. What they are like is conjecture. Advances in medicine might logically yield long-lived extra-terrestrials who have mechanical substitutions of so many organs that they become cyborgs. And many a science fiction story depicts the eventual takeover of a planet’s biological species by intelligent machines.

And what constitutes “life” anyway? One struggles to state a clear definition. Common definitions include: “the presence of an ordered assembly of molecules which uses energy to metabolize, creates structures, grows and reproduces, all in the face of locally defeating the inevitable increase in over-all entropy.” NASA once adopted a working definition as “a self-sustained chemical system capable of undergoing Darwinian evolution.” You can probably imagine some examples that would contradict or render incomplete nearly any given definition. Perhaps it is more akin to what a U. S. Supreme Court Justice called the definition of pornography: “you’ll know it when you see it.” I certainly hope that the robotic probes we are sending to Mars and the moons of Jupiter and Saturn will know it if and when they see it.
--
Richard M. Lawn
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Message 2039198 - Posted: 20 Mar 2020, 17:18:27 UTC

Thank you, Dr. Lawn, for another interesting essay. How life arose-- essentially order from disorder-- is an intriguing topic. This tendency seems to be built into the universe, from even the earliest times. Even before life began, galaxies, stars, and planets had to organize themselves from a chaos of matter and energy, in order to prepare the way for life.

This universal tendency for order to emerge from disorder can be demonstrated by computer-based cellular automata. It even appears in a curiously humble physical model: A jar containing paper clips, with the ends bent out slightly to form crude hooks, is shaken. The paper clips spontaneously form chains , and even more complex, cross-linked connections. Even a low number of paperclips, and a brief shaking can accomplish this. We can draw from this demonstration that instances of such organization are not at all rare.
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Message 2040424 - Posted: 26 Mar 2020, 0:00:04 UTC - in response to Message 2038992.  

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