DI claims evolutionists have "no comment" on RNA World -- but they rejected my comment!

Over on the DI blog, David Klinghoffer wrote:

Darwinists on RNA World: “No Comment” David Klinghoffer August 19, 2011 6:00 AM | Permalink

Darwinists routinely complain about our policy on comments here: we allow them when we do, and don’t when we don’t. The impression is that they are just itching to have at our science writers. Yet we opened comments the other day on Jonathan M.’s thoughtful take-down of the RNA World hypothesis as a solution to the origins-of-life conundrum – and no critics showed up for the party. Only friendlies did so. Come on, gentlemen! Jonathan’s conclusion:

Michael Marshall’s New Scientist article does not even come close to demonstrating the feasibility of the RNA world hypothesis, much less the origin of the sequence-specific information necessary for even the simplest of biological systems. Since information is a phenomenon uniformly associated with intelligent causes, it follows inductively that intelligent design constitutes the best – most causally sufficient – explanation for the information-content of the hereditary molecules DNA and RNA.

Go there and let us know why you disagree.

Hmm, that’s quite odd, since I’ve been commenting on JonathanM’s pieces occasionally over the last few weeks, mostly at Uncommon Descent.

The common feature of JonathanM’s posts is above-average research for an IDist, but way below-par research in terms of actual scholarship. He knows just enough to seem informed, but doesn’t bother to look up any of the actual research on the questions he asks – he just assumes that whatever problem with evolution that he thinks up over breakfast is some crushing objection that none of the experts has ever thought about before.

Usually this boils down to not a God-of-the-Gaps-Human-Knowledge argument, but a God-of-the-Gaps-in-JonathanM’s-Knowledge argument, which is, I think, an even more devastating mistake than the usual God-of-the-Gaps argument.

Anyhow, as background to the below, a week or two ago JonathanM made a post on UD 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 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.

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 Klinhoffer – an answer to your question about why there were no challenges to JonathanM.

JonathanM – Well, I don’t see a forthright admission that you made a mistake last week when you claimed that the OOL was impossible because it was hard to assemble RNA monomers from separate bases, sugars, and phosphates – an argument which was disproven in 2009 by Sutherland’s work – but I’ll take it.

Other points:

“Since information is a phenomenon uniformly associated with intelligent causes, it follows inductively that intelligent design constitutes the best – most causally sufficient – explanation for the information-content of the hereditary molecules DNA and RNA.”

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.

Your overall article is taking a very strange line. Basically, you admit that the RNA world hypothesis has made all kinds of advances – better, simpler syntheses have been discovered, better replicases have been discovered, RNA enzymes have been found in all sorts of places in biology where they aren’t strictly necessary given that proteins should work better as enzymes, etc. But, then you say we should ignore all these advances in the research program, they haven’t solved everything so it’s all worthless and we should believe that God created life with a miracle as the explanation instead.

Also, this is a peculiar argument:

Moreover, as I documented in a review of Nick Lane’s book, 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. When the nucleotides are present in high concentrations, it is conceivable that they would spontaneously polymerize (this, of course, ignores the problem of sequence-specificity, but we can leave that aside). In the case of low concentration, conversely, the RNA breaks down into its constituent nucleotides. But here’s the thing: Synthesis of the novel RNA strand requires that nucleotides be consumed (thus decreasing their concentration). The pool of nucleotides, therefore, would have to be perpetually replenished at a rate faster than it is consumed. Please see my response to Nick Lane’s notions of the origin of life in hydrothermal vents for a rebuttal to a common attempted resolution of this problem.

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!

As for the origin of replication, given the right building blocks, not every paper deals with every issue, and it’s not fair to criticize papers devoted to specific topics like RNA chemistry for not addressing other specific topics – at least, not without being a responsible scholar and having a look at the literature for other papers that address your problem. Here’s one. And let’s not have “oh but there’s no chemistry” – that what the chemistry papers are for.

Prevolutionary dynamics and the origin of evolution

Martin A. Nowak† and Hisashi Ohtsuki

• Author Affiliations

Program for Evolutionary Dynamics, Department of Organismic and Evolutionary Biology, Department of Mathematics, Harvard University, Cambridge, MA 02138

Communicated by Clifford H. Taubes, Harvard University, Cambridge, MA, July 14, 2008 (received for review May 31, 2008)

Abstract

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.

Both this work and the replicase work assume that the key event in the origin of life was the origin of one self-replicating molecule, but others have pointed out that a collection of smaller short-sequence RNAs might be a more likely route, if it turns out that a replicase has a large minimum size (which we don’t actually know). People have barely started exploring these possibilities in the RNA world. How can you just throw up your hands and say “God/ID didit!” when it’s clear that research progress is being made?