Frequently Asked Questions: Abiogenesis (Biopoesis)

Organization: evolv-o-tron, inc.
From: Deaddog <>
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What is abiogenesis? It is commonly construed to mean the origin of 'life' from 'non-life,' but both terms are vague and difficult to define. While we recognize 'life' (dogs) when we see it, and think that we recognize 'non-life' (rocks), this distinction may not have been as clear cut on the Archean Earth. Therefore, I choose to talk about the propagation of heritable information: basically, how chemical patterns (dogs and rocks) are replicated and selected over time.

The Physical Setting

(really not my forte, so I'm brushing up a bit first)

The Earliest Replicators

Modern theorists can be broken up into several different camps. Apologies to those camps that I miss.

Clay People: Minerals can 'replicate' their crystalline structure. Their chemical pattern may change with time; for example, as a clays 'grow' they incorporate ions into their structure. If the environment in which a clay is found changes, and the source of ionic 'food' also changes (magnesium gives way to, say, aluminum), the matrix can continue to grow, but will be chemically different. Because of the difficulties inherent in imagining how organic replicators arose, some theorists, notably A.G. Cairns-Smith, have advanced the following hypothesis: inorganic replicators (clays) seeded organic replicators (of whatever sort). This hypothesis is called "genetic takeover." The serious book is "Genetic Takeover and the Mineral Origins of Life, Cambridge University Press, New York, 1982, but the fun book is "Seven Clues to the Origin of Life," written in an easy-to-follow Sherlockian style.

Advantages: No need for large pool of complex organic molecules to start; can be gradually added. Deftly avoids all questions of the sort 'where did the ribose come from'

Disadvantages: No evidence nor plausible mechanism for 'genetic takeover.' However, it should be noted that clays have been seen to catalyze a number of prebiotic reactions.

Chemical cycles: Chemical cycles replicate their components and are self-sustaining. Interacting cycles can arise [e.g. D<-->B<-->C<-->D added to A<-->B<-->C<-->A], are equivalent to 'mutations,' and are themselves heritable. The most prolific popularizer of these theories is G~nter W{chtershe~ser, a German patent attorney with a strong background in chemistry (Micro Rev., 52, 452 (1988)). His most basic chemical pathway is related to a reductive Krebs cycle, is dependent on pyrite, fool's gold, and gives rise to a rich tapestry of additional reactions. Modern cells again took over the chemical reactions by blebbing off organic coacervates from mineral surfaces.

Advantages: Can derive almost all modern metabolism; genetic (as opposed to chemical) inheritance does not become involved until quite late; most reactions are postulated to occur in, well, slime layers on the surface of rocks (pyrite). This both reduces the dimensionality and dilution problems associated with normal prebiotic chemistry, and provides an 'identity' for chemical organisms (i.e., 'self'= your rock).

Disadvantages: Some slight evidence for the ur- cycle, but the chemistry is pushed well beyond the bounds of anything known today. If he turns out to be right it will be an intellectual achievement ranking with the Theory of Relativity. My personal assessment is that the reactions have been severely strained to produce 'modern' compounds and pathways, while it seems far more likely that the chemical cycles that initially evolved may have looked nothing like what exists today. That is, this theory seems to be guided by biological preconceptions rather than chemical plausibility.

Genetic replicators. Note that these are actually a subset of chemical cycles, but rely on some form of structural complementarity rather than reactivity for their propagation. Although all styles of hypothesized replicators exist, most are based on Watson-Crick style base complementarity. However, see work from Rebek's lab for replicators that have been designed de novo (JACS, 112, 1249 (1990)). Short, self-replicating nucleic acid molecules have been constructed by both von Kiedroswki (Angew. Chem.(English) 98, 932 (1986)) and Orgel (Nature, 327, 346 (1987)). This is why I always get a kick out of folks babbling on about how we don't yet have self-replicating nucleic acids, this will be the key to life, etc., etc., etc. What they mean, of course, is that we don't have a nucleic acid polymerase that can use nucleotide triphosphates ... which were unlikely to have been around in abundance in the prebiotic milieu anyway.

Advantages: Obvious and direct relation to modern life. Polymers can act as catalysts for their own replication and can create what Eigen has called 'hypercycles' (Eigen, Naturwissenschaften, 65, 341 (1978) is the classic paper in this field).

Disadvantages: 'Food' tends to be relatively unstable molecules (see, for example, Pace, Cell, 65, 531 (1991)) that are prepared in extremely low yield by prebiotic pathways currently known. In order to get around this, there are a wide range of nucleic acid 'like' compounds that are proposed to have preceded real nucleic acids on the evolutionary stage (Joyce, Nature, 338, 217 (1989) for a brilliant review).

Overall: it is generally believed that one of these replicators must have evolved to a nucleic acid based genetic system. The initial complexity of the metabolism in which the original nucleic acid replicators arose is open to question; for chemical cycles it can be quite complex, for genetic replicators it was almost certainly dirt simple.

Extrapolating Backwards

It is extremely important to try to discern how these replicators would have led to modern systems. What do we know about the ancestors of modern life? Despite the almost complete lack of a conventional fossil record, a great deal. In fact, the molecular details of the progenitor of modern life are almost certainly much better known than, say, the physiological or morphological characteristics of a protobovoid. This is because every organism on the planet contains a wealth of metabolic fossils that have been far better preserved by genetic replication than any mineral fossilization could have hoped to have achieved. I will elaborate with only one example, but there are many (Benner, Ellington, and Tauer, PNAS, 86, 7054 (1989) is a tour de force, but you may disagree with many of their conclusions).

There are three domains of life: archaebacteria, eubacteria and eukaryotes. For practical purposes, these three domains can be considered to have diverged from one another at more or less the same time (that is, the evolutionary distance between any two of them is huge). NAD is the redox equivalent of metabolism, just as ATP is the energy equivalent (I realize this is an oversimplification, but let it stand for the nonce). The structure of the NAD is the same in the three domains. Therefore, the last common ancestor of modern life had NAD.

Using logic similar to this, we can discern which molecules, pathways, and cofactors are ancient, and which are modern. Taken together, these inferences allow us to draw a picture of the last common ancestor of modern life, a cell that existed roughly 2.5 billion years ago. This cell had DNA, RNA, proteins, and a complex metabolism. It had probably invented translation relatively recently, and may still have had many reactions that were catalyzed by nucleic acid enzymes, as opposed to proteins.

The Big Gap

What happened between ca. 3.5 billion years ago, when the first replicators arose, and 2.5 billion years ago, when a cell that was in many respects similar to those that course our veins today existed? This is the field of abiogenesis: what mechanism is most likely to move through this tortuous 1 billion year history. There are literally hundreds of hypotheses competing to fill this era. For example, if you choose to believe Wachtershauser, I can draw you a detailed and complete map of virtually every major evolutionary event at the molecular level over the last 3.5 billion years.

But, and I can't emphasize this strongly enough, all of these hypotheses are based on one theory, the theory of evolution. Because we know how modern nucleic acid replicators (viruses and cells) and their attendant metabolisms have evolved, and because we know that the earliest replicators evolved towards a nucleic acid-based replication system (the last common ancestor of modern life), we can extrapolate into this gap. The extrapolations that prebiotic chemists / abiogeneticists perform are no different than the extrapolations that paleontologists perform in tying together the lineages of creatures long dead. We use molecular bones, but they are no less real.

Organization: evolv-o-tron, inc.
From: Deaddog <>
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I have posted the mini-FAQ in the hopes of providing some snippets of evidence for those who say there are none. Perhaps this will sway some of you, perhaps not.

I have tried to avoid advancing or advocating specific mechanisms for abiogenesis because I still believe that the following should be enough for us all:

Evolution is both a theory and a fact. In accepting this, we must follow its tenets to their logical conclusion. Organisms evolve; their lineages can be traced. Their lineages lead back to a cell. Just as all cells evolved from this cell, so this cell must have evolved from something. The cell must have evolved from some set of molecules. These molecules can be seen to evolve even today. All of the events that led from the molecules to the cell were governed by the theory of evolution. It is the same theory that governs the evolution of all organisms, indeed of all self-replicating systems.

Some of you clearly agree with this, and yet still insist on dividing abiogenesis from 'evolution.' I can live with Robert Derrick's argument, which is a very good one: in essence, the propaganda value of evolution as a theory is greater in the absence of abiogenesis. I agree wholeheartedly. But know this: this position is intellectually dishonest.

I am surprised and disheartened to find that abiogenesis is in fact an acid test of how you view evolution. Either you can extrapolate into the past based solely on *the intellectual force of the theory alone* or else you must caterwaul for facts and assurances. Darwin had nothing like the molecular techniques available today, and yet he could of necessity imagine a 'warm little pond' (I am doubtlessly historically inaccurate in claiming this).

Yes, with facts you can batter the religious Creationists. But it is not the facts that give you explanatory power; they merely give you evidence. It is the theory that explains the facts. And I fear that any mound of facts will not erase the new vitalism that I find amongst those who study evolutionary biology. The position that abiogenesis deals with non-living things, and therefore is separate from evolution automatically imparts a mystical force to organisms that separates them from other evolving systems, such as the molecules of which they are composed. This seems a philosophical point, and so it is. But I think it has consequences in how you defend the theory and fact of evolution against religious Creationists. Perhaps I am mistaken, but I think that while you would insist on removing them from a biology class, you might be quite comfortable in allowing them to teach an origins class that gave 'equal time' to chemical evolution, panspermia, and divine intervention of a non-sectarian sort -- since we really don't *know* which of these it was, right?

Certainly I am being alarmist; but the recent attempts to gain a toehold in social sciences classes can easily be expanded to natural science based on precisely this sort of philosophical distinction. I post for my own amusement, certainly, but I believe it matters a great deal whether or not abiogenesis is considered a logical and necessary consequence of the theory of evolution.


[Thank you, Eric, for your concern, but I have said this about as many ways as I can think to say it. I fear that some folks will just have to remain ... incorrect. Diatribes: off. Responses (on this thread) by E-mail only.]