The Origin of Life: An RNA World? - Evolution News & Views

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The Origin of Life: An RNA World?

Previously on ENV, I published a review of a recent article that appeared in New Scientist concerning the RNA world scenario with regard to the origin of life. Nick Matzke at Panda's Thumb has since responded with a critique of my argument. This is my response to his remarks.

The Sutherland Research
Matzke writes,

...a week or two ago JonathanM made a post on [Uncommon Descent] that claimed various half-baked problems for the natural origin of life, one of which was that the assembly of RNA was difficult, because nature would have to separately [sic] sugars, bases, and phosphates separately, and then assemble them. The only problem with this argument, whatever its original merits, is that it was directly falsified by the Sutherland Group's famous experiments in 2009. Oops! I pointed this out on UD, and although it took some tooth-pulling, got some UD people to more-or-less admit that JonathanM made a mistake there. JonathanM, though, seems to be acting like his sure-thing takedown of the origin of life from a few weeks ago never happened.
This is a curious statement, not least because the Sutherland research was specifically addressed in my previous article. It's also surprising that Matzke states, "...although it took some tooth-pulling, [I] got some UD people to more-or-less admit that JonathanM made a mistake there." This simply isn't the case, as you can see by reading the comments thread there.

Anyhow, let's return to the Sutherland research. What are its key problems?

1) Only pyrimidine (not purine) ribonucleotides were produced.

2) The problem of sequence-specificity remains unsolved.

3) The chirality problem remains unsolved.

4) The researchers have not produced RNA which can do anything of biological significance.

5) The whole experimental setup is permeated with clever manipulations (e.g., tweaking pH and temperature as needed along the way; using UV radiation at the right times and durations to remove problematic side-products, etc.) that are unlikely to resemble pre-biotic conditions.

Casey Luskin has previously written on the subject here. In that article, Casey quotes organic chemist Dr. Charles Garner:

As far as being relevant to OOL, the chemistry has all of the usual problems. The starting materials are "plausibly" obtainable by abiotic means, but need to be kept isolated from one another until the right step, as Sutherland admits. One of the starting materials is a single mirror image for which there is no plausible way to get it that way abiotically. Then Sutherland ran these reactions as any organic chemist would, with pure materials under carefully controlled conditions. In general, he purified the desired products after each step, and adjusted the conditions (pH, temperature, etc.) to maximum advantage along the way. Not at all what one would expect from a lagoon of organic soup. He recognized that making of a lot of biologically problematic side products was inevitable, but found that UV light applied at the right time and for the right duration could destroy much (?) of the junk without too much damage to the desired material. Meaning, of course, that without great care little of the desired chemistry would plausibly occur. But it is more than enough for true believers in OOL to rejoice over, and, predictably, to way overstate in the press.
Indeed, even some non-ID origin-of-life researchers have conceded that this paper doesn't reflect plausible pre-biotic conditions.

As a 2009 news article on the website of the Royal Society noted,

However, Robert Shapiro, professor emeritus of chemistry at New York University disagrees. 'Although as an exercise in chemistry this represents some very elegant work, this has nothing to do with the origin of life on Earth whatsoever,' he says. According to Shapiro, it is hard to imagine RNA forming in a prebiotic world along the lines of Sutherland's synthesis.

'The chances that blind, undirected, inanimate chemistry would go out of its way in multiple steps and use of reagents in just the right sequence to form RNA is highly unlikely,' argues Shapiro. Instead, he advocates the metabolism-first argument: that early self-sustaining autocatalytic chemosynthetic systems associated with amino acids predated RNA.

Nick Matzke continues his response to me by saying,
All of this may explain why, when I posted the following comment to JonathanM's RNA World post at the DI website -- hours after the original RNA World post was published, if I recall correctly -- it said "comment received," but the moderators never approved it. So there you go, David Klinghoffer -- an answer to your question about why there were no challenges to JonathanM.
We are sorry that Matzke's comment seems to have been lost. We have no records of the comment submission, and it certainly was not deleted. We are not aware of what became of it.

Gene Duplication as a Source of Novelty?
So, let's turn to the substance of Matzke's comment. After re-iterating the already-addressed point about the Sutherland research, he writes:

It's not true that "information is a phenomenon uniformly associated with intelligent causes." The natural processes of gene duplication plus mutation and selection produces new genetic information all the time. This explodes the core of the ID argument, by your own admission of what the argument is.
Matzke's point here has been addressed so many times on ENV and elsewhere that there is no need to go into detail again. On this subject, I refer readers to Douglas Axe's published bacterial population model. In that paper, Axe argues that the model of gene duplication and recruitment only works if very few changes are need to acquire novel selectable utility or neo-functionalization. If a duplicated gene is neutral, then the maximum number of mutations (not inclusive of the duplication itself) that a novel innovation in a bacterial population can require is up to six. If the duplicated gene has a slightly negative fitness cost, the maximum number drops to two or fewer. See also my comments on gene duplication here and here, as well as Casey Luskin's comments here, here, here, and here.

Many problems face the gene duplication-and-divergence model of neo-functionalization. One associated difficulty, often overlooked, is that the change in amino acid sequence, to give a protein a new function, must be accompanied by changes in regulatory sequences. Consider, for example, the evolution of the globins, one of the most commonly cited textbook examples of gene duplication. It is thought that at some point, a gene encoding for haemoglobin was duplicated. One copy retained its original function (carrying oxygen in the blood), while the other mutated into myoglobin: a protein, similar to haemoglobin, used in muscle to help extract oxygen from the blood for use by the muscle. Myoglobin's function is made possible by its higher affinity for oxygen. The modifications of the protein's amino acid sequence, in order for it to be converted from haemoglobin to myoglobin, would have needed to be accompanied by changes in its regulatory sequences in order to ensure that the myoglobin was produced in the muscle where it is needed, rather than in bone marrow where the red blood cells are produced. Myoglobin present in red blood cells would not provide a selective advantage. In fact, it would be harmful to the organism because it would bind too tightly to oxygen and not release it to the tissues.

At any rate, enough has been said. Regardless of whether gene duplication and divergence represents a viable mechanism for the production of novel genetic information, such a means cannot be invoked to account for the origin of biological information in the first place. Indeed, natural selection, in effect, presupposes the prior existence of information on which to feed. But since this discussion is concerned with the origin of biological information in the first place, this detour is not so relevant here.

A Peculiar Argument?
Matzke subsequently quotes my statement that ribonucleotides "will only polymerize if the nucleotides are present at high concentrations," describing it as "a peculiar argument." This is interesting, since Nick Lane (a leading origin-of-life theorist) acknowledges the very same problem in his book Life Ascending: The Ten Great Inventions of Evolution, though he attempts a solution that I addressed in my previous critique of his take on the origin of life.

Nick Lane writes in his book,

...alkaline hydrothermal vents are riddled with interconnecting pores. Thermal gradients produce two types of current, which circulate through these pores, convection currents (as in a boiling kettle) and thermal diffusion (the dissipation of heat into cooler waters). Between them, these two thermal currents gradually silt up the lower pores with many small molecules, including nucleotides. In their simulated hydrothermal system, the concentration of nucleotides reached thousands and even millions of times the starting level. Such high levels should comfortably condense nucleotides into RNA or DNA chains.
There are basically two major problems with this view. First, there is the lack of stability of organic molecules at high temperatures. Second, if the origin of life took place in an aqueous solution of pre-biotic monomers, then -- according to Le Chateliers Principle -- the presence of a reaction product will significantly decrease the reaction rate. Le Chatelier's principle essentially entails that, in a reversible reaction, the reaction will uniformly progress in the direction required to sustain equilibrium between the concentration of reactants and products. Since the product of the condensation reaction between nucleotides to form nucleic acids is water, and since under aqueous conditions this product would be present in a higher concentration compared to any other species in the reaction mix, Le Chatelier's principle would cause the reaction to favour the hydrolysis side (which breaks up the nucleic acids back into nucleotides). It is not possible to polymerize an appreciable amount of monomers into polymers in an aqueous solution. Thus, the necessary polymerization step in the reaction could not take place in water. The same is true of the polymerisation of amino acids to form peptides.

Some might argue that the heat from hydrothermal vents would provide a localized area with sufficient energy such that this principle could be overcome, enabling nucleotides to form nucleic acids, and amino acids to form dipeptides. This, of course, runs back into the conundrum of the instability of organic materials at high temperatures. In order for this difficulty to be circumvented, one needs to posit a repeated cycle of heating and drying. However, the problem is that all the water must be removed, but care must be taken not to over-heat -- and thus rapidly break down -- the synthesized polymers. As ENV's Casey Luskin notes here, "This would have to be a very fine balancing act that would also requires rapid input of organic material to overcome the rate at which the heat would destroy the molecules."

Nick Matzke writes that,

You seem to view the natural production of certain molecules as a one-shot deal. Why? If a geochemical process produced the molecules once it could produce them again -- in fact, that would be more likely than not producing them again, given similar conditions. In fact, the most common situation in nature would be that molecules would exist at some kind of equilibrium. For example, phosphate, one of the relevant molecules here, dissolves out of certain rocks at a certain rate, and then is consumed by reactions or precipitation at a certain rate. If some polymerization process starts that begins to consume phosphate, it's not as if the phosophate will suddenly magically stop coming out of the rocks. And yet for some strange reason you confidently assume otherwise!
Matzke seems to miss the point of the argument here. Phosphorous is a subunit of nucleotides (the others being ribose sugar and the nitrogenous base). But I wrote that "the conundrum of making the individual ribonucleotides is only part of the story. They will only polymerize if the nucleotides are present at high concentrations." Matzke thus appears to conflate the synthesis of nucleotides and their subsequent polymerization.

The Origin of Replication
Nick Matzke concludes his reflections by drawing my attention to Nowak and Ohtsuki (2008), who summarise the contents of their research in the abstract as follows:

Life is that which replicates and evolves. The origin of life is also the origin of evolution. A fundamental question is when do chemical kinetics become evolutionary dynamics? Here, we formulate a general mathematical theory for the origin of evolution. All known life on earth is based on biological polymers, which act as information carriers and catalysts. Therefore, any theory for the origin of life must address the emergence of such a system. We describe prelife as an alphabet of active monomers that form random polymers. Prelife is a generative system that can produce information. Prevolutionary dynamics have selection and mutation, but no replication. Life marches in with the ability of replication: Polymers act as templates for their own reproduction. Prelife is a scaffold that builds life. Yet, there is competition between life and prelife. There is a phase transition: If the effective replication rate exceeds a critical value, then life outcompetes prelife. Replication is not a prerequisite for selection, but instead, there can be selection for replication. Mutation leads to an error threshold between life and prelife.
In the paper, they report,
Traditionally, one thinks of natural selection as choosing between different replicators. Natural selection arises if one type reproduces faster than another type, thereby changing the relative abundances of these two types in the population. Natural selection can lead to competitive exclusion or coexistence. In the present theory, however, we encounter natural selection before replication. Different information carriers compete for resources and thereby gain different abundances in the population. Natural selection occurs within prelife and between life and prelife. In our theory, natural selection is not a consequence of replication, but instead natural selection leads to replication.
It's not entirely clear in what sense the authors are using the term "information," nor that they understand it. They tell us that "prelife is a generative system that can produce information." We are also told that "Evolution needs a generative system that can produce unlimited information. Evolution needs populations of information carriers." They also tell us on the first page that they "can define a prebiotic chemistry that can produce any binary string and thereby generate, in principle, unlimited information and diversity." Since when was a set of random strings of characters a sound definition of "information" -- at least in any meaningful sense as applied to biology?

The authors here seem to indiscriminately consider any polymer that out-competes the others, by virtue of being more abundant, as a forerunner to the origin of life. Note the assumption here that all sequences are equally conducive to life. How can this be justified? There comes a point when the abundant polymer must contain functional information. Indeed, the simplest micro-organisms that we know require a minimum of two or three hundred genes (or a few hundred thousand base pairs of DNA).

The model proposed in this paper is highly theoretical and speculative -- with no substantive practical experimental research to back it up.

Summary & Conclusion
We have explored just a small handful of the confounding difficulties confronting the chemical origin of life. This is not a god-of-the-gaps argument, as Matzke claims, but rather a positive argument, based on our uniform and repeated experience of cause-and-effect. It is not based on what we don't know, but on what we do know: that intelligence is a necessary and sufficient condition for the production of novel complex and functionally specified information. The design inference is based on sound and conventional scientific methodology. It utilizes the historical or abductive method and infers to the best explanation from multiple competing hypotheses.