David Deamer on Wet-Dry Cycles in Abiogenesis

David W. Deamer is a professor of biomolecular engineering at the University of California, Santa Cruz, where his research has included the self-assembly of membrane structures in the origin of life. He is co-inventor of the nanopore technology for DNA sequencing (U.S. Patent 6,015,714 [PDF]), and has investigated organic compounds found in the Murchison meterorite that fell in Australia in 1969, finding lipid-like molecules that can self-assemble into vesicles.

Deamer is author of two books on abiogenesis, the technical Assembling Life: How Can Life Begin on Earth and Other Habitable Planets and popular Origin of Life: What Everyone Needs to Know. He makes the case that volcanic hot springs may be the most probable site for the origin of terrestrial life, given the presence of nutrients, precursor molecules, and a wet-dry cycle that can concentrate molecules in solution to allow reactions to proceed.


I haven’t the time to invest in his argument. I must wonder if he addresses the near-impossible statistical likelihood of functional proteins/nucleic acids arising from random processes.


I haven’t read either of Prof. Deamer’s books, but from the conversation I believe he leans toward the “metabolism first” view of abiogenesis, as argued by Freeman Dyson in Origins of Life. In these models, vesicles form naturally from self-assembled membranes of ambiphilic molecules (this can be observed in the laboratory), and, from the concentrated soup at the volcanic vent, an auto-catalytic cycle of molecules is contained in some of these vesicles, which is able to perform a primitive metabolism using nutrients that pass in through the vesicle wall, producing excreta that pass out. This cycle will cause growth, and may initially reproduce through nothing more complicated than the vesicle stretching out and splitting in two as it reaches a critical size. This extremely simple system, made entirely of molecules already found at its site of origin, would still be a replicator and subject to natural selection, with faster and more prolific replicators coming to dominate the population. This would then set the stage for a “genetic takeover” where some information-storing molecule, such as small RNA precursors, acting both as information storage and enzymes, would be incorporated and give vesicles containing it an advantage. From there, evolution would drive more permanent storage, accurate replication, and regulation of metabolism.

The blurb for Dyson’s book does a pretty good job of summing up the idea.

The majority view is that life began with replicating molecules, the precursors of modern genes. The minority belief is that random populations of molecules evolved metabolic activities before exact replication existed and that natural selection drove the evolution of cells toward greater complexity for a long time without the benefit of genes. Dyson analyzes both of these theories with reference to recent important discoveries by geologists and chemists, aiming to stimulate new experiments that could help decide which theory is correct. This second edition covers the impact revolutionary discoveries such as the existence of ribozymes, enzymes made of RNA; the likelihood that many of the most ancient creatures are thermophilic, living in hot environments; and evidence of life in the most ancient of all terrestrial rocks in Greenland have had on our ideas about how life began.

The main advantage of the metabolism-first theory is that a metabolic autocatalytic cycle does not need the extreme accuracy of replication that the DNA/RNA/protein mechanism requires to avoid an error catastrophe. While a replication error rate of 5% would quickly doom a DNA sequence of only 100 base pairs (and all existing organisms have far larger genomes), Dyson estimates a metabolism-only cell could withstand error rates as high as 25%, while providing an environment in which more accurate replication would have a selective advantage.


The common sense question is – if life evolved spontaneously somehow, somewhere, under some conditions, then why did it not happen a thousand times? It is a big planet, after all. Why is it not happening today? Why are we not inundated with evidence of multiple occurrences of the spontaneous generation of life?

This is not to claim that life did not appear spontaneously. Maybe it did. But why was it apparently a one-time occurrence? Without a coherent explanation of that, the theory seems rather iffy.


Maybe it did. The record we have is fragmentary and very hard to read in any detail, and any really successful replicator would quickly (in geological timescales) overrun the world, leaving little to no room for any subsequent independent development and possibly destroying/eating it’s less successful cousins. On the other hand, maybe next month someone digs up some samples that reflect a different path that got snuffed out by the victor.

I’m also open to Sir Fred’s panspermia theory that it could have developed elsewhere and landed here. Then the long odds shift from initial development to transmission to Earth.


Very simple metabolism-first life may, indeed, be spontaneously generated to this day in volcanic hot springs, mid-ocean vents, or wherever it was the ancestor to all terrestrial life appeared so long ago. But that primitive replicator would be slow to reproduce and utterly undefended against the multitude of DNA-based microbes in its environment which, with the advantages conferred by billions of years of highly competitive evolution, would perceive it as a little bag full of rich nutrients. “Hey, I’m alive! Isn’t this neat?” CHOMP!

There’s also the problem that the tools we use to screen for new microbes, almost all of which look for DNA and/or RNA, would not detect metabolism-first organisms or consider them alive. We would only detect them if they reproduced in sufficient numbers to be obvious at the macroscopic scale and, given the competition from modern organisms, that is very improbable.


We had a post here on 2022-03-25, “Is There a Shadow Biosphere on Earth?” about the possibility that Earth may be home to one or more forms of life (shadow biosphere) which are sufficiently different in their metabolism and genetic information transfer that they escape detection by the tools we use to survey for new species of microbes. This might especially be the case if organisms from the shadow biosphere primarily inhabit environments thought inhospitable to known life such as deep underground, mid-ocean vents, or in Antarctic ice.

We did not discover extremophile bacteria and archaea until the 1960s and 1970s, and they were, by comparison, abundant and right under our noses, using conventional metabolic pathways and genetics.

For years, it has been suggested that desert varnish might be an example of a shadow biosphere, but it is now believed to be formed chemically and not a living organism.


That is a testable hypothesis. It is clearly possible to set up sterile lab conditions where the spontaneous generation of life could be demonstrated – probably for a small fraction of the money spent over the years on SETI. Why has that not been done?


He has shown that the largest and most species-rich group of lichens are not alliances between two organisms, as every scientist since Schwendener has claimed. Instead, they’re alliances among three. All this time, a second type of fungus has been hiding in plain view.

“There’s been over 140 years of microscopy,” says Spribille. “The idea that there’s something so fundamental that people have been missing is stunning.”

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Jack Szostak, winner of the Nobel Prize in Physiology or Medicine in 2009 and now a professor at the University of Chicago and leader of the Origins of Life Initiative is working on precisely this. His Szostak Lab page describes this work as follows:

We are interested in the chemical and physical processes that facilitated the transition from chemical evolution to biological evolution on the early earth. As a way of exploring these processes, our laboratory is trying to build a synthetic cellular system that undergoes Darwinian evolution. Our view of what such a chemical system would look like centers on a model of a primitive cell, or protocell, that consists of two main components: a self-replicating genetic polymer and a self-replicating membrane boundary. The job of the genetic polymer is to carry information in a way that allows for both replication and variation, so that new sequences that encode useful functions can be inherited and can further evolve. The role of the protocell membrane is to keep these informational polymers localized, so that the functions they encode lead to an advantage in terms of their own replication or survival. Such a system should, given time and the right environment, begin to evolve in a Darwinian fashion, potentially leading to the spontaneous emergence of genomically encoded catalysts and structural molecules.

Of course, any laboratory experiment, however clever its designers, cannot explore all of the possibilities of niche environments on Earth, running in parallel over hundreds of millions of years, which may have eventually stumbled upon the first replicator.

probably for a small fraction of the money spent over the years on SETI

What is about funding for SETI that seems to irritate people? Essentially all of the money spent on SETI over its history has been private funds contributed to nonprofit groups operating on a shoestring. The NASA SETI program which was funded in 1992 was killed within one year due to ridicule in Congress. Besides, investigating the origin of life on Earth, where we know, after all, it did get started and now exists, has precious little to do with the existence or nonexistence of communicating technological civilisations elsewhere in the galaxy or searches for biosignatures and technosignatures indicating the presence of extraterrestrial life, whether microbial or technological.


Personally, I am not irritated at all by SETI – although prudence would suggest that we confine ourselves to listening only, since there is no assurance that the civilization on the other end would be interested in buying us a Coke.

The point is that, as a human race, we seem much more interested in trying to find extra-terrestrial aliens than in exploring the testable issue of whether life can spontaneously appear from a chemical brew. Those two propositions seem to be the two sides of the same coin – either receiving a message from space or producing life in the lab would clearly answer the question about how common life is in the universe. But one side of that coin is sexy, and the other side (which is totally within our control) gets little attention.


Oh, it has gotten some serious attention by Stephen C Meyer. He has brought serious thought and analysis to the problem, including serious study of the probability of information required for first life arising spontaneously. His serious work has been ignored by the scientism faithful - as “pseudo-science”. The fact is that in any other endeavor, the presence of new information is always the result of mind, a creator of information. “Evolution” does not apply to chemical soups. I’m not sure it applies to replicating “metabolism first” hypotheses either. It immediately runs into the information problem Meyer so clearly and scientifically elucidates. It begins the minute RNA/DNA enter the picture.


The question is, how does the “mind” (whatever that is) create the new information? Maybe the mind does it by a process of massively parallel random variation and recombination, combined with selection through filters trained from previous experience and/or hard wired from birth (“instinct”). This is, after all, not unlike the process used by the recently successful generative AI programs. But, more interestingly, it’s essentially the same way evolution works in a biosphere: massively parallel search among individuals and species, random variation due to copying errors, recombination by sexual reproduction and lateral gene transfer among microorganisms, and selection by the environment and competition with other individuals and species.

An interesting perspective on the origin of novelty in organisms is presented in Andreas Wagner’s book Arrival of the Fittest: How Nature Innovates, which I am in the process of reading. Wagner is a pioneer in computational genomics, and has mapped the multidimensional space of metabolic pathways and proteins in microorganisms. The number of possible phenotypes defined by the metabolic pathways by which a bacterium can obtain energy and carbon from nutrients is around 2^{5000}\approx 10^{1500}, which is a number vastly larger than the number of subatomic particles in the visible universe (\approx 10^{80}). Yet if you arrange these reactions as vertices of a 5000-dimensional hypercube and then explore which neighbourhood can be reached from a given vertex by changing only one reaction at a time (which is equivalent to being connected by an edge between the vertices), you discover the neighbourhoods are vast and extend through a large space of the metabolic hypercube.

For example, a computer experiment started with the reactions that E. Coli uses to synthesise all of its sixty or so essential biomass molecules from glucose and then explored how many adjacent metabolisms (arrived at by changing just one reaction) were viable, defined as synthesising the same products. What was found is the total number of viable metabolisms an alternative E. Coli could use to live off glucose numbered more than 10^{750}, with the most distant sharing only 20% of the reactions used by the original bacterium.

The same experiment may be repeated on proteins, and one finds that starting with an 80 amino acid protein used to bind ATP and again changing just one amino acid at a time, there were 10^{93} equivalently functional proteins reachable from the starting point, all by a series of single residue changes of the kind a random mutation causes.

This means the capacity for innovation inherent in these biological systems is enormous and, more importantly, drastically different molecular structures exist which perform the same biological function, all of which can be arrived at by a series of single-step changes of precisely the kind evolution produces. But these functionally identical variants can have very different properties at the level of the organism, such as tolerance to temperature, chemical environment, ability to resist damage from toxins, etc. So it is plausible that constant random incremental variation and selective feedback allows innovation of never-before explored structures which increase adaptation to the ever-changing environment.

I’m only half way through the book. I’ll reserve judgement until I finish it.


Looking forward to your review of that book, sir!

The only axe I have to grind on evolution is that it seems like an incomplete hypothesis, just a part of the real story. How do we reconcile single-step changes at the molecular level (entirely plausible) with the apparent fossil evidence of punctuated equilibrium (big steps) at the macro level of evolution?

Sure, we can shrug and say that the fossil record is clearly incomplete, but that seems unsatisfactory.


One of the best books on this topic is:

Dawkins goes into a series of examples, like the evolution of the eye - and shows the now-forgotten intermediate steps that led to what might seem to be a punctuated equilibrium.

Even in technology, we are forgetting all the intermediate steps and partial failures it took to get to say a pocket touchscreen computer.

As for definitions of life, this is a really good article:

I’m not sure we should put too much weight on “body plans” as seen in the fossil record when it comes to incremental evolution’s ability to innovate. As we’ve learned since genomes of a wide variety of organisms have become available, the DNA sequence of a genome is not, alone, the blueprint for the large scale structure of an organism, but rather its expression is controlled through the process of gene regulation, which forms a complex network of chemical interactions where regulatory molecules not only serve to activate or inhibit the transcription of genes into proteins, but also act upon one another, creating structures similar to complex Boolean expressions and nested IF statements in computer programming. This means that a small, incremental change to the genome that expresses a regulatory protein can result in large-scale, macroscopic changes to the organism that is produced.

This is demonstrated dramatically in insects, amphibians, and marine invertebrates which have larval forms that bear little resemblance to the adult organism. In fact, if both forms were observed in isolation, most taxonomists would consider them completely unrelated. And yet the larval and adult form have completely identical genomes, with the macroscopic differences due to hormones triggering gene regulation in expressing the two different forms from the same genome.

Since life has many ways at the molecular level of accomplishing the same function, all reachable by changes of only one step at a time that do not affect viability of the organism, organisms may be able to change their overall form by incremental changes in regulatory portions of the genome, which become frozen once a population which ends up better adapted to its environment becomes established as distinct from its progenitor.


That is a good example. Jellyfishes, for example, apparently have about 7 different phases of life with different forms. We might think of that as the organism being told – Now turn to Chapter 4 of the pre-existing manual, and implement the new instructions. But how did that pre-existing manual come into being?

I have no problem with the concept of natural evolution – because every dog, cow, horse, pig, corn plant we see is the product of very unnatural human-directed evolution through selective breeding. No question that selective breeding works. But for all the patience of hundreds of generations of farmers & animal breeders, human beings have not been able to create any distinctly new form of life. All we can do is emphasise desired qualities which are already there in the DNA – which are already in the pre-existing manual, so to speak. The implication is that Darwinian evolution is an incomplete hypothesis.


I am not at all able to understand this approach to information generation. It is clear to me that you are quite expert at this and can interpret this arcane approach. I have also read your review of Signature in the Cell, an explanation I can follow and which has persuaded me it is substantially correct. When you have digested Wagner’s book, might you consider comparing the persuasive merits of the two? I ask this because of your ability to comprehend both attempts at understanding, as well as your ability to explain complex things to those of us less able to understand the primary sources.

For whatever reason, the first origin of life is a pressing issue for me. Of all the mysteries whose answers I wish for before I exit, this heads the list.

ADDENDUM: I should add that, I not only read John’s review of Signature in the Cell. I read the book three times. It had a profound effect on my understanding.