Science v Intelligent Design: Wolf and Koonin on the origin of the translation system

Posted 10 October 2007 by PvM

In a recent paper, authors Yuri Wolf and Eugene Koonin present a hypothesis on the origin of the translation system and show how science proceeds. I am encouraging ID proponents to present a similarly detailed explanation based on the foundational concepts of Intelligent Design. The authors explain how the problem is neither trivial and yet can be resolved:

The origin of the translation system is, arguably, the central and the hardest problem in the study of the origin of life, and one of the hardest in all evolutionary biology. The problem has a clear catch-22 aspect: high translation fidelity hardly can be achieved without a complex, highly evolved set of RNAs and proteins but an elaborate protein machinery could not evolve without an accurate translation system. The origin of the genetic code and whether it evolved on the basis of a stereochemical correspondence between amino acids and their cognate codons (or anticodons), through selectional optimization of the code vocabulary, as a "frozen accident" or via a combination of all these routes is another wide open problem despite extensive theoretical and experimental studies. Here we combine the results of comparative genomics of translation system components, data on interaction of amino acids with their cognate codons and anticodons, and data on catalytic activities of ribozymes to develop conceptual models for the origins of the translation system and the genetic code.

In other words, any hypothesis needs to address the catch-22 scenario as well as incorporate the scientific knowledge gathered so far. In their explanations, these scientists use a main guiding principle

Our main guide in constructing the models is the Darwinian Continuity Principle whereby a scenario for the evolution of a complex system must consist of plausible elementary steps, each conferring a distinct advantage on the evolving ensemble of genetic elements. Evolution of the translation system is envisaged to occur in a compartmentalized ensemble of replicating, co-selected RNA segments, i.e., in a RNA World containing ribozymes with versatile activities. Since evolution has no foresight, the translation system could not evolve in the RNA World as the result of selection for protein synthesis and must have been a by-product of evolution drive by selection for another function, i.e., the translation system evolved via the exaptation route. It is proposed that the evolutionary process that eventually led to the emergence of translation started with the selection for ribozymes binding abiogenic amino acids that stimulated ribozyme-catalyzed reactions.

In other words, the scenario needs to be plausible in the sense that each step confers a distinct advantage, and since evolution has not foresight, the translation system must have evolved via an exaptation route. In addition to presenting various plausible scenarios, the authors also acknowledge our level of ignorance (or in ID speak 'complexity') and provide us with experimental tests that can help resolve several aspects of their scenario. The authors explain how the origin of 'complex biological systems' is not only a classical topic in evolutionary science but also a principal focus of attack by "anti-darwinists of all ilk".

The origin of complex biological systems is a classical topic in evolutionary biology and, probably, the principal object of attacks of anti-darwinists of all ilk, including the notorious Intelligent Design movement. The gist of the criticisms is that many biological systems are not just complex but "irreducibly complex" and, as such, could never evolve via the Darwinian mechanism of gradual, stepwise adaptive change because intermediate stages of evolution would have no selective value and so could not be fixed. Darwin himself was perfectly aware of the problem and its dimensions and addressed it in one of the most famous passages of the Origin, the one on the evolution of the vertebrate eye [1]. The solution offered by Darwin and developed ever since in numerous works of evolutionary biology was straightforward in principle and extremely ingenious when it came to details.

So what challenge is facing the evolutionary biologist?

When an evolutionary biologist strives to explain the origin of a truly novel system that is seen only in its elaborately complex state and, at face value, appears to be irreducibly complex, the task is much harder.

The scenario needs to be based on the logical premise that "evolution has no foresight"

Because evolution has no foresight, no system can evolve in anticipation of becoming useful once the requisite level of complexity is attained. Instead, the evolving system must have a selectable function(s) distinct from the modern one, a possibility recognized by Darwin [1] and emphasized by Gould in the concept of exaptation, that is, reassignment of function in the course of evolution [11,12].

The steps need to be "mangeable"

In either case, the general Darwinian principle applies: evolution must proceed via consecutive, manageable steps, each one associated with a demonstrable increase in fitness. Darwin did not use a specific term for this crucial tenet of evolutionary biology; we will call it the Continuity Principle, following the recent insightful discussion of this issue by Penny [8]. The developments in the 150 years since Darwin taught us to be more flexible about this principle than he was. It is no longer prudent to demand, as Darwin did, that all evolutionary changes are "infinitesimal"; some genome modifications may have had a substantial one time effect on fitness, e.g., those that involve horizontal gene transfer, gene loss, or genome rearrangement [13].

and the steps need not be selective since evolutionary science has shown how neutral or even slightly deleterious steps can still become fixed in the genome.

Furthermore, it cannot be demanded that every change is selectively advantageous because neutral or even slightly deleterious mutations can be fixed by drift, especially, in small populations [9,14]. Nevertheless, these newly discovered factors of evolution, however important by themselves, are but modifications of the Continuity Principle – evolution of complex systems still needs to be deconstructed into successive steps and explained in a Darwinian way.

The authors explain that the chicken and the egg problem of the "Central Dogma" can be resolved via an RNA-alone step, also known as the RNA world. This conclusion is founded on many scientific findings

The unique property of RNA that makes it a credible, indeed, apparently, the best candidate for the central role in the primordial replicating system is its ability to combine informational and catalytic functions. This notion has been greatly boosted by the study of ribozymes (RNA enzymes), which was pioneered by Cech and coworkers' discovery, in 1982, of the autocatalytic cleavage of the Tetrahymena rRNA intron [38], and by the demonstration, in 1983, by Altman and coworkers, that RNAse P is a ribozyme [39]. Since the time of these seminal discoveries, the study of ribozymes has evolved into a vast, expanding research area (at the time of this writing, March 1, 2007, the keyword 'ribozyme' retrieves 4883 documents from the PubMed database; for recent reviews, see [40-43]).

Of course, the RNA world scenario is further strengthened by the fact that the RNA world can still be found in living organisms

It is often noted that the RNA World is not just a concept supported by the catalytic prowess of ribozymes: while overshadowed by the multitude of proteins with catalytic and structural functions, the RNA World still lurks within modern life forms

The authors conclude

To recapitulate, three independent lines of evidence converge in support of a major role of RNA, and in particular, RNA catalysis at the earliest stages of life's history, and are compatible with the reality of a complex, ancient RNA world that was first postulated by Woese, Crick, and Orgel on purely logical grounds. First, comparative analysis of the protein components of the translation machinery and their homologs involved in other functions strongly suggests that extensive diversification of the protein world took place at the time when the translation system was comprised, primarily, of RNA. Second, several classes of ribozymes operate within modern cells, and their properties are compatible with the notion that they are relicts of the ancient RNA world. Third, while limited in scope and, obviously, inferior in catalytic activity compared to protein enzymes [41], ribozymes have been shown or, more to the point, evolved to catalyze a remarkable variety of reactions including those that are central to the evolution of translation (Table 1).

The authors then continue, in good scientific fashion, to play the 'devil's advocate' and explore common objections and weaknesses of this scenario. While ID proponents typically perceive this step as a weakness, science has come to rely on it as a strength. The authors then address the origin of the genetic code, which is strongly linked with the origin of the translation system

To understand how translation might have emerged, the nature and origin of the codon assignments in the universal genetic code are crucial.

Typically there are three proposed scenarios 1. Stereo-chemistry 2. Selection 3. Historical contingency: also known as 'frozen accident' Although the authors seem to prefer the 'frozen accident', one of the reviewers, the well known genetic code researcher, Bob Knight, observes that the novelty of their scenario does not depend on the exact route through which the genetic code evolved. In another posting I will attempt to discuss the various scenarios and how they stack up, needless to say, science has uncovered plausible scenarios and supporting evidence, even though the origin of the genetic code is likely a historical event hundreds if not thousands of million of years in our past. How can they do this? By using plausible scenarios based on chemistry, physics and an understanding of plausible prebiotic atmospheres. (See for instance Signature of a Primitive Genetic Code in Ancient Protein Lineages, in J Mol Evol. 2007 Oct 6)

The genetic code is the syntactic foundation underlying the structure and function of every protein in the history of the biological world. Its highly ordered degenerate complexity suggests an incremental evolution, the result of a combination of selective, mechanistic, and random processes. These evolutionary processes are still poorly understood and remain an open question in the study of early life on Earth. We perform a compositional analysis of ribosomal proteins and ATPase subunits in bacterial and archaeal lineages, using conserved positions that came and remained under purifying selection before and up to the most recent common ancestor. An observable shift in amino acid usage at these conserved positions likely provides an untapped window into the history of protein sequence space, allowing events of genetic code expansion to be identified. We identify Cys, Glu, Phe, Ile, Lys, Val, Trp, and Tyr as recent additions to the genetic code, with Asn, Gln, Gly, and Leu among the more ancient. Our observations are consistent with a scenario in which genetic code expansion primarily favored amino acids that promoted an increase in polypeptide size and functionality. We propose that this expansion would have been critical in the takeover of many RNA-mediated processes, as well as the addition of novel biological functions inaccessible to an RNA-based physiology, such as crossing lipid membranes. Thus, expansion of the genetic code likely set the stage for the transition from RNA-based to protein-based life.

The authors then continue to propose their scenario as well as experiments to test the scenario. In their discussion, the authors clarify their guiding principles, the speculative nature of their claims, and yet they also point out how their claims follow from simple guiding principles of science. Their proposed explanation is based on constraints

Thus, our main incentive with the present analysis was to deconstruct the formidable problem of the emergence of translation into a series of plausible and manageable steps, in accordance with the Continuity Principle. We believe that, in doing so, we achieved a somewhat greater level of detail and coherence than any of the previous models we are aware of. Importantly, in constructing this model, we were both constrained and driven by: i) comparative-genomic data, ii) experimental data on amino-acid-codon recognition, iii) experimental data on the diverse catalytic activities of ribozymes.

The authors then repeat their guiding principles

Discussion and conclusion The status of the model: incentives and constraints The scenarios for the origin of the translation system and the genetic code outlined here are both sketchy and highly speculative. Why, then, bother building such conceptual, qualitative models at all? The justification for this kind of theorizing can be succinctly put in the short phrase: we have to get from there to here. There being the early, cooling earth with no complex organic molecules, and here being a minimally complex genetic system with modern-type translation, transcription, and replication machineries, a system that would be subject to biological evolution much like modern organisms. The replication and transcription problems are, at least, logically relatively straightforward, even if hard from the chemical point of view, inasmuch as no new principles, beyond base complementarity, and enzymatic catalysis need to be invented. Thus, plausible, even if conflicting, accounts of the emergence of these systems have been derived from comparative-genomic data and evolutionary reasoning [70,140-144]. There is, however, a crucial snag about these models: they all rely on a pre-existing translation system. And the origin of the translation system is far from being a trivial matter. The main difficulty is not even its complexity per se but the necessity to invent a new principle, that of the genetic code, the correspondence between the a priori unconnected sequences of nucleotides and amino acids. It might not be much of an exaggeration to note that, at least, at first glance, the origin of the translation system evokes the scary specter of irreducible complexity. Thus, our main incentive with the present analysis was to deconstruct the formidable problem of the emergence of translation into a series of plausible and manageable steps, in accordance with the Continuity Principle. We believe that, in doing so, we achieved a somewhat greater level of detail and coherence than any of the previous models we are aware of. Importantly, in constructing this model, we were both constrained and driven by: i) comparative-genomic data, ii) experimental data on amino-acid-codon recognition, iii) experimental data on the diverse catalytic activities of ribozymes. Comparative-genomic analysis indicates that an elaborate translation system, comparable to the modern one in terms of fidelity and efficiency, has evolved within the RNA world. Indeed, extensive diversification of many protein folds occurred before the advent of some of the essential components of the modern translation system, such as aaRS and translation factors. Before the emergence of these dedicated proteins, the translation system must have been a machine comprised primarily, if not exclusively, of RNA. The only conceivable alternative, that the primordial translation system employed a different, currently, extinct complement of essential protein factors, inevitably leads to infinite regression. Thus, it seems to be a virtually inevitable conclusion that the ancient, RNA-only translation system was comparable in efficiency to the modern one. This might seem paradoxical and even not credible at a superficial glance. However, a quick reflection suggests that: i) the skeleton of the modern translation system actually consists of RNA, with the proteins being elaborations, however numerous and important, and ii) logically, it hardly could have been otherwise: indeed, in order to switch to a new type of constituents (proteins), biological systems needed the means to produce them accurately. It is conceivable and, indeed, likely that peptides produced by the first, RNA-based proto-translation systems provided positive feedback leading to hypercycle formation (Figs. 4, 6). However, this primitive version of translation must have been quite sloppy and hardly could master production of anything beyond relatively short peptides. Evolution of the (nearly) complete set of tRNAs was a pre-requisite for achieving the fidelity required to kick off protein evolution in earnest. In our description of the model, the alternative scenarios based on CRM, ARM, and FAM are considered on equal footing. As discussed above, the currently available data are too ambiguous to conclude which of these models for the origin of coding is most likely. However, it should be noted that, important as they are in terms of the actual physico-chemical underpinning of the code, the differences between CRM, ARM, and FAM do not translate into major modifications of the evolutionary scenario. Indeed, the central principles remains the same, i.e., specific recognition of amino acids by proto-tRNAs such that an amino acid is paired with the cognate anticodon with sufficient reliability. Lasting principles and ephemeral details The models presented here were deliberately constructed at the level of considerable detail -at the risk of getting many, perhaps, most aspects wrong – in order to provide a proof of principle, i.e., to illustrate a plausible sequence of selectively advantageous steps along the path from the RNA world to the modern-type translation system. This being said, there seem to be several underlying principles that are likely to stand regardless of further developments. We briefly recapitulate these: 1. Evolution having no foresight, selection for translation per se is not feasible. Translation must have evolved as a by-product of selection for some other function, i.e., via the exaptation route. 2. Given that the essence of translation is the intimate link between RNA and proteins, it seems most likely that, in some form, this connection existed from the very beginning of the evolutionary path from the RNA World to translation. Thus, the proposed starting point, i.e., stimulation of ribozymes by amino acids and peptides seems to be a strong, almost, logically required, candidate for this role (see also [145]). 3. Synthesis of peptides directly on an RNA template is stereochemically unfeasible. Hence adaptors must have been part of the primordial translation system from the start. Accordingly, from the very onset of translation, adaptors have been key to the establishment of the genetic code. These ancestral adaptors, although, in all likelihood, smaller and simpler than modern tRNAs, must have been endowed with catalytic capacities lacking in the latter, i.e., they would have to catalyze specific self-aminoacylation with the cognate amino acids. 4. The primordial translation system was dominated by RNA although peptides might facilitate its functioning. However, the fidelity of this primordial, (nearly) RNA-only translation system must have been comparable to that of modern translation systems, considering that extensive protein evolution took place prior to the diversification of the proteins that are essential for the modern translation. Problems and testability The current scenario for the evolution of translation in the RNA World faces formidable difficulties because, although the ribozyme catalysis of the elementary reactions required for translation has been demonstrated experimentally (Table 1), the required complex RNA-mediated functions have not. The crux of the problem seems to lie in the postulated catalytic adaptors that would have to possess a notable spectrum of capabilities including, in addition to the apparently feasible specific recognition of amino acids and self-aminoacylation, the ordered binding to the progenitor of the large subunit (RL), and at a subsequent stage, recognition of a specific region in the progenitor of the small subunit (RS). With regard to RL and RS themselves, ribozyme stimulation by amino acids and peptides has been demonstrated but, beyond that, the postulated properties of these molecules remain hypothetical. It seems that a focused experimental effort aimed at the construction/selection of ribozymes with the properties of the postulated T RNAs, in particular, their postulated interaction with other, more complex ribozymes, could provide crucial evidence in support of this or a similar scenario for the evolution of translation. Although the individual ribozyme-catalyzed reactions involved in the postulated scheme are feasible, the succession of multiple evolutionary steps that appear to be required for the emergence of translation might be legitimately viewed as far fetched, particularly, considering the inevitably inefficient ribozyme-mediated replication that must have been prevalent in the RNA World. Be as it may, this is, at present, our best effort to develop a conceptual model for the origin of translation. Elsewhere, one of us (EVK) examines a radical alternative [17].

As far as experimental verification

It seems that a focused experimental effort aimed at the construction/selection of ribozymes with the properties of the postulated T RNAs, in particular, their postulated interaction with other, more complex ribozymes, could provide crucial evidence in support of this or a similar scenario for the evolution of translation.

And that my friends is how science works. Since I do not want to pretend to be speaking for Intelligent Design, I invite ID proponents to share with us their guiding principles, and show how their scenario explains the origin of the translation system better, given the constraints and known data. Read the full article: On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization Biol Direct 2007; 2: 14.

78 Comments

PvM · 10 October 2007

As a reminder, let me present the ID thesis: Design is the set theoretic complement of regularity and chance. In other words, design is that which remains once known (important distinction) natural processes have been eliminated. This of course means that there could be yet unknown pathways that have been missed by science, but for the moment let's ignore this real possibility. So what can ID propose? It can show that the proposed pathway is too improbable given the known boundary conditions, as well as known laws of physics, chemistry. But that would not provide us with a competing explanation. ID could propose that the 'complexity' of the problem, which is defined to be the negative log(2) of the probability that translation can be explained via regularity and chance is too small and that since the system is obviously 'specified', it must have been designed. However, there are some problems with this approach. Namely, design does not require a designer.

Before I proceed, however, I note that Dembski makes an important concession to his critics. He refuses to make the second assumption noted above. When the EF implies that certain systems are intelligently designed, Dembski does not think it follows that there is some intelligent designer or other. He says that, "even though in practice inferring design is the first step in identifying an intelligent agent, taken by itself design does not require that such an agent be posited. The notion of design that emerges from the design inference must not be confused with intelligent agency" (TDI, 227, my emphasis).
— Ryan Nichols

In other words, design is but a first step in identifying an intelligent agent. Design itself, without some additional data, cannot be sufficient as an hypothesis for a designer. So what can ID do to resolve this conundrum? Remember how the authors of the paper constrained their hypothesis with guiding principles, remember how the authors constrained their hypothesis with known data? The solution for ID seems 'straightforward', they have to constrain the design and the design(er) to allow them to propose a scientifically relevant hypothesis. Now science has proposed various methods to constrain the designer. For instance in criminology, science uses concepts of means, motives, opportunity, as well as physical evidence, eye witnesses to conclude design and hypothesize a designer. Even in SETI, science uses a narrow band signal, a simple signal which is known to originate from our planet, caused by intelligent beings and not found (as far as we can tell) in nature.

Any signal less than about 300 Hz wide must be, as far as we know, artificially produced. Such narrow-band signals are what all SETI experiments look for.

I hope that my outline for what a competing explanation from ID has to look like has been helpful in understanding why many have come to accept that ID is scientifically without content. Of course, I encourage any ID proponent to present their best hypothesis, in a manner that allows us to compare their explanation to the explanation suggested by Wolf and Koonin.

PvM · 10 October 2007

To show that calculating a small probability for the proposed scenario (not a trivial calculation and quite a task for any ID proponent, a task which ID proponents have been reluctant to take up btw), is not evidence of design either, let me provide the reader with the following scenario.

What is the probability that the proposed scenario is incomplete or totally wrong? Let's accept for the moment that the probability of the scenario being right is extremely small, what is the probability that design is right versus the probability that an unknown pathway explains the origin of the translation system? ID cannot provide a probability for their design scenario so we will unlikely be able to determine what is more likely, design or ignorance.
In other words, even lacking any scenario, ID cannot even compete with our ignorance.

On ISCID, a poster named Gedanken has done much to educate us as to why the design inference in most cases is extremely unreliable, contrary to the claims by Dembski. So, lacking any detailed scenarios based on constraints, ID cannot even compete with our ignorance.

Although, let this not be a reason for ID proponents to show that my arguments are incorrect. After all, I fear no peer review :-)

TheBlackCat · 10 October 2007

I am encouraging ID proponents to present a similarly detailed explanation based on the foundational concepts of Intelligent Design.

That's easy: "poof"

PvM · 10 October 2007

We have our first candidate :-)

CJO · 10 October 2007

No, no. It's got to be 'sciency.'

The system arose due to a highly-specimificated endogenous poofulation event.

John Farrell · 10 October 2007

How about:

poof ^ 2 (squared)

Robby · 10 October 2007

PvM:

Very interesting post. You do realize that Eugene Koonin rejects the scenarios presented in the paper, right? See http://www.biology-direct.com/content/2/1/15
http://www-ctp.mit.edu/cosmo/y0607/koonin_abs.html

His efforts in this paper was to try to imagine the best possible scenario for a gradual, step-by-step, Darwinian pathway to the coded translation apparatus. Yet he himself rejects this best scenario as far-fetched and he looks to principles beyond Darwinism to explain it. He states in the paper you cite:

"Even under the best case scenario, the RNA world does not appear to have potential to evolve beyond very simple "organisms". To attain greater complexity, invention of translation and the Protein Breakthrough were required. However, the selective forces underlying the emergence of the translation system in the RNA World remain obscure, and tracing the path to translation is extremely hard. This lack of clarity with regard to the continuity of evolution from the RNA World to an RNA-protein world can be construed as a second major objection against the RNA World as a crucial stage of life's evolution, an objection, perhaps, even more prohibitive than the first one, dealing with the imperfection of ribozymes. A radical alternative, "no RNA World" hypothesis, is considered elsewhere [17]. In the rest of this article, we discuss possible ways to derive the translation from the RNA World through a path of evolution adhering to the Continuity Principle...
Although the individual ribozyme-catalyzed reactions involved in the postulated scheme are feasible, the succession of multiple evolutionary steps that appear to be required for the emergence of translation might be legitimately viewed as far fetched, particularly, considering the inevitably inefficient ribozyme-mediated replication that must have been prevalent in the RNA World. Be as it may, this is, at present, our best effort to develop a conceptual model for the origin of translation. Elsewhere, one of us (EVK) examines a radical alternative [17]."

IDers would do well to follow Koonin's pattern of trying to think from the opposite side of the table instead of just trying to destroy evolutionary arguments. But Koonin, like IDers, argues that what we know about translation and evolution suggest that such a system could not be evolved by Darwinian means. He makes *exactly* the same predictions as an IDer would in his other paper on the origin of translation:

"The strong form of the present hypothesis, i.e., the notion that the breakthrough stage in the history of life was a primitive coupled replication-translation system (Fig. 2), is falsifiable. Such a system should be construed as the upper bound of complexity for the breakthrough stage (Fig. 1). As soon as the possibility of biological evolution at a lower level of complexity, e.g., in the RNA world, is demonstrated and the route from the RNA world to the translation system is established, either experimentally or, at least, in a compelling model, the origin of a complex system with coupled replication and translation by chance/anthropic selection will be, effectively, ruled out. A demonstration that life independently emerged on several planets in our O-region will have the same effect. In the Appendix, I provide a rough, toy calculation of the upper bound of the probability of the emergence of a coupled replication-translation system in an O-region – this probability is, indeed, vanishingly small....This point can be illustrated by deliberately naïve, toy calculations of the upper bound of the probability of the emergence of different versions of the breakthrough system by chance. In the Appendix, I present such calculations for two versions, the RNA World with a ribozyme replicase, and the coupled translation-replication system. Under the assumptions of this toy model (idealized to the extreme in that an unrealistically high rate of abiogenic RNA production is assumed), the emergence, by chance, of a ribozyme replicase in a finite universe consisting of a single O-region like ours, in principle, could be considered. However, any significant increase in complexity would call for a different cosmological model. In particular, the emergence of a coupled replication-translation system is unlikely to the extent of being, effectively, impossible. For such a complex system to be a viable candidate for the breakthrough stage, an infinite multiiverse, such as the one depicted by MWO or, in the very least, a universe with a vast number of O-regions, is, indeed, a must....Despite considerable experimental and theoretical effort, no compelling scenarios currently exist for the origin of replication and translation, the key processes that together comprise the core of biological systems and the apparent pre-requisite of biological evolution. The RNA World concept might offer the best chance for the resolution of this conundrum but so far cannot adequately account for the emergence of an efficient RNA replicase or the translation system.....General assumptions: an O-region contains 1022 stars and every 10th star has a habitable planet, hence 1021 habitable planets (undoubtedly, a gross over-estimation because, in reality, most stars have no planets at all, let alone habitable ones). Each planet is the size of earth and has a 10 kilometer (106 cm) thick habitable layer; hence the volume of the habitable layer is 4/3π[R3-(R-l)3] ≈ 5 × 1024 cm3, where R is the radius of the planet and l is the thickness of the habitable layer. RNA synthesis occurs in 1% of the volume of the habitable layer, i.e., a volume V ≈ 5 × 1022 cm3 is available for RNA synthesis (undoubtedly, a gross over-estimation because, in reality, there would be very few "RNA-making reactors"). Let the concentration of nucleotides in volume V and the rate of the synthesis of RNA molecules of size n (a free parameter depending on the specific model of the breakthrough stage; hereinafter n-mer) be 1 molecule/cm3/second (a gross overestimate for any sizable molecule; furthermore, the inverse dependence on n, which is expected to be strong, is disregarded). The time available after the Big Bang of the given O-region (as an upper bound) of all planets in it is 1010 years ≈ 3 × 1017 seconds. Then, the number of uniquen-mers "tried out" during the time after the Big Bang is:

S ≈ 5 × 1022 × 1021 × 3 × 1017 ≈ 1.5 × 1061.

Let us assume that, for the onset of biological evolution, a unique n-mer is required. The number of such sequences is N = 4n ≈100.6n.

Then, the expectation of the number of times a unique n-mer emerges in an O-region is: E = S/N = 1.5 × 1061/100.6n and n = log(E × 1.5 × 1061)/0.6.

Substituting E = 1, we get n ≈102 (nucleotides). Note that, because n is proportional to logS, the estimate is highly robust to the assumptions on the values of the contributing variables; e.g., a order of magnitude change in S will result in an increase or decrease of n by less than 2 nucleotides.

A ribozyme replicase consisting of ~100 nucleotides is conceivable, so, in principle, spontaneous origin of such an entity in a finite universe consisting of a single O-region cannot be ruled out in this toy model (again, the rate of RNA synthesis considered here is a deliberate, gross over-estimate).

The requirements for the emergence of a primitive, coupled replication-translation system, which is considered a candidate for the breakthrough stage in this paper, are much greater. At a minimum, spontaneous formation of:

- two rRNAs with a total size of at least 1000 nucleotides

- ~10 primitive adaptors of ~30 nucleotides each, in total, ~300 nucleotides

- at least one RNA encoding a replicase, ~500 nucleotides (low bound)is required. In the above notation, n = 1800, resulting in E <10-1018.

In other words, even in this toy model that assumes a deliberately inflated rate of RNA production, the probability that a coupled translation-replication emerges by chance in a single O-region is P < 10-1018. Obviously, this version of the breakthrough stage can be considered only in the context of a universe with an infinite (or, in the very least, extremely vast) number of O-regions.

The model considered here is not supposed to be realistic by any account. It only serves to illustrate the difference in the demands on chance for the origin of different versions of the breakthrough system (see Fig. 1) and hence the connections between these versions and different cosmological models of the universe."

In other words Eugene Koonin states that there are no evolutionary scenarios for the origin of translation that are feasible, and that the probability of a replication-translation apparatus occurring by chance is infinitesemally small. I personally am not sure that you could simplify his breakthrough system to just a replicator (since ribozymes need nucleotides and nucleotides must have proteins in order to be synthesized, as there is no such demonstration that ribozymes can synthesize and maintain an activated nucleotide batch on their own; also in order for translation and replication to occur at all, ATP is necessary, yet the adenine in this system is contingent on proteins for synthesis, or at least a complex ribozyme system with metabolism that could not be there before the onset of replication when it was necessary), but even if you could, getting from a replicator to a full blown translation apparatus can not and has not been fixed by plausible selective steps. At least according to Koonin.

I am not sure that Koonin is as good of an example for this as you think he is.

harold · 10 October 2007

This is all very interesting. I would clarify one thing.

It seems highly reasonable indeed to assume that a series of events that led from chemical precursors to clearly living cells would be analagous to biological evolution, in the sense that intermediate structures would arise from natural variance events, that would be followed in some cases by positive selection for a variant, then further variation of that variant, and so on.

However, we should be clear about differentiating abiogenesis, which surely involved such evolution-like processes, from actual biological evolution of cellular and post-cellular life. The latter can be observed in the present and understood at a very detailed mechanistic level. Lack of a single clear, mechanistically detailed theory or hypothesis of abiogenesis does not in any way detract from the massive amounts of evidence for biological evolution.

Also a minor nitpick. The author's state...

"In other words, the scenario needs to be plausible in the sense that each step confers a distinct advantage".

I suppose it depends on how one defines a "step", but certainly, some intermediates need not be positively selected for ("provide an advantage" in subjective human value terms) per se, but could merely not be excessively selected against, increase in the population through a process analagous to genetic drift, and be present as a source of future variation that would be selected for.

Robby · 10 October 2007

PvM:

S ≈ 5 × 1022 × 1021 × 3 × 1017 ≈ 1.5 × 1061.

Let us assume that, for the onset of biological evolution, a unique n-mer is required. The number of such sequences is N = 4n ≈100.6n.

Then, the expectation of the number of times a unique n-mer emerges in an O-region is: E = S/N = 1.5 × 1061/100.6n and n = log(E × 1.5 × 1061)/0.6.

- two rRNAs with a total size of at least 1000 nucleotides

- ~10 primitive adaptors of ~30 nucleotides each, in total, ~300 nucleotides

- at least one RNA encoding a replicase, ~500 nucleotides (low bound)is required. In the above notation, n = 1800, resulting in E <10-1018.

I am not sure that Koonin is as good of an example for this as you think he is.

Robby · 10 October 2007

PvM:

"The strong form of the present hypothesis, i.e., the notion that the breakthrough stage in the history of life was a primitive coupled replication-translation system (Fig. 2), is falsifiable. Such a system should be construed as the upper bound of complexity for the breakthrough stage (Fig. 1). As soon as the possibility of biological evolution at a lower level of complexity, e.g., in the RNA world, is demonstrated and the route from the RNA world to the translation system is established, either experimentally or, at least, in a compelling model, the origin of a complex system with coupled replication and translation by chance/anthropic selection will be, effectively, ruled out. A demonstration that life independently emerged on several planets in our O-region will have the same effect. In the Appendix, I provide a rough, toy calculation of the upper bound of the probability of the emergence of a coupled replication-translation system in an O-region – this probability is, indeed, vanishingly small....This point can be illustrated by deliberately naïve, toy calculations of the upper bound of the probability of the emergence of different versions of the breakthrough system by chance. In the Appendix, I present such calculations for two versions, the RNA World with a ribozyme replicase, and the coupled translation-replication system. Under the assumptions of this toy model (idealized to the extreme in that an unrealistically high rate of abiogenic RNA production is assumed), the emergence, by chance, of a ribozyme replicase in a finite universe consisting of a single O-region like ours, in principle, could be considered. However, any significant increase in complexity would call for a different cosmological model. In particular, the emergence of a coupled replication-translation system is unlikely to the extent of being, effectively, impossible. For such a complex system to be a viable candidate for the breakthrough stage, an infinite multiiverse, such as the one depicted by MWO or, in the very least, a universe with a vast number of O-regions, is, indeed, a must....Despite considerable experimental and theoretical effort, no compelling scenarios currently exist for the origin of replication and translation, the key processes that together comprise the core of biological systems and the apparent pre-requisite of biological evolution. The RNA World concept might offer the best chance for the resolution of this conundrum but so far cannot adequately account for the emergence of an efficient RNA replicase or the translation system.....General assumptions: an O-region contains 1022 stars and every 10th star has a habitable planet, hence 1021 habitable planets (undoubtedly, a gross over-estimation because, in reality, most stars have no planets at all, let alone habitable ones). Each planet is the size of earth and has a 10 kilometer (106 cm) thick habitable layer; hence the volume of the habitable layer is 4/3pi[R3-(R-l)3] ≈ 5 × 1024 cm3, where R is the radius of the planet and l is the thickness of the habitable layer. RNA synthesis occurs in 1% of the volume of the habitable layer, i.e., a volume V ≈ 5 × 1022 cm3 is available for RNA synthesis (undoubtedly, a gross over-estimation because, in reality, there would be very few "RNA-making reactors"). Let the concentration of nucleotides in volume V and the rate of the synthesis of RNA molecules of size n (a free parameter depending on the specific model of the breakthrough stage; hereinafter n-mer) be 1 molecule/cm3/second (a gross overestimate for any sizable molecule; furthermore, the inverse dependence on n, which is expected to be strong, is disregarded). The time available after the Big Bang of the given O-region (as an upper bound) of all planets in it is 1010 years ≈ 3 × 1017 seconds. Then, the number of uniquen-mers "tried out" during the time after the Big Bang is:

S ≈ 5 × 1022 × 1021 × 3 × 1017 ≈ 1.5 × 1061.

Let us assume that, for the onset of biological evolution, a unique n-mer is required. The number of such sequences is N = 4n ≈100.6n.

Then, the expectation of the number of times a unique n-mer emerges in an O-region is: E = S/N = 1.5 × 1061/100.6n and n = log(E × 1.5 × 1061)/0.6.

- two rRNAs with a total size of at least 1000 nucleotides

- ~10 primitive adaptors of ~30 nucleotides each, in total, ~300 nucleotides

- at least one RNA encoding a replicase, ~500 nucleotides (low bound)is required. In the above notation, n = 1800, resulting in E <10-1018.

I am not sure that Koonin is as good of an example for this as you think he is.

wamba · 10 October 2007

Don't worry, it will sound more 'sciency' once we convert to the appropriate Latin terminology:

"Oof-pay."

wamba · 10 October 2007

Hey "Robby," try using the Preview button.

Robby · 10 October 2007

PvM:

IDers would do well to follow Koonin's pattern of trying to think from the opposite side of the table instead of just trying to destroy evolutionary arguments. But Koonin, like IDers, argues that what we know about translation and evolution suggest that such a system could not be evolved by Darwinian means. He makes exactly the same predictions as an IDer would in his other paper on the origin of translation:

I am not sure that Koonin is as good of an example for this as you think he is.

MememicBottleneck · 10 October 2007

Let's see, I think the IDers believe (at least some of them, since nothing reliable is written down) in multiple "kinds" poofed during the "Precambrian Explosion" with subsequent micro-evolution. How about polypoofimicromorphifacation.

And yes, I did take the name from lurking on this site. This site and talkorigins has been a great help in dealing with my creo office mate.

PvM · 10 October 2007

Robby, I believe that you suggestion that Koonin rejects these scenarios is incorrect, he however accepts that there remain significant problems, just as he outlined in the paper I quoted.

So let's see how ID does compared to Koonin, shall we? If, as you seem to suggest, the Wolf & Koonin scenario is a poor choice then surely ID can provide us with a better one?

Popper's Ghost · 10 October 2007

But Koonin, like IDers, argues that what we know about translation and evolution suggest that such a system could not be evolved by Darwinian means. He makes exactly the same predictions as an IDer would

That's utterly clueless. Aside from the misuse of the word "prediction" and the absurd claim about what an IDer would do, Koonin doesn't argue any such thing in the quoted paragraph.

Frank J · 10 October 2007

I am encouraging ID proponents to present a similarly detailed explanation based on the foundational concepts of Intelligent Design.
— PvM

I have yet to get an answer to the most basic questions regarding what the last design actuation event was, and roughly when it occurred, so I predict that, in the rare case that you do get an answer, it will not be "poof," but "You're asking me to play a game...I won't take the bait...It's not ID's task to match your pathetic level of detail..."

Popper's Ghost · 10 October 2007

In other words Eugene Koonin states that there are no evolutionary scenarios for the origin of translation that are feasible

Be wary of people claiming "in other words". No words even close to that appear in the quoted paragraph.

Popper's Ghost · 10 October 2007

Let's look at the words that Koonin actually does use:

the selective forces underlying the emergence of the translation system in the RNA World remain obscure, and tracing the path to translation is extremely hard

"obscure" and "extremely hard [to trace]" are not anything like "not feasible".

In the rest of this article, we discuss possible ways to derive the translation from the RNA World through a path of evolution adhering to the Continuity Principle… Although the individual ribozyme-catalyzed reactions involved in the postulated scheme are feasible, the succession of multiple evolutionary steps that appear to be required for the emergence of translation might be legitimately viewed as far fetched, particularly, considering the inevitably inefficient ribozyme-mediated replication that must have been prevalent in the RNA World. Be as it may, this is, at present, our best effort to develop a conceptual model for the origin of translation.

"are feasible" is not the same as "not feasible". "legitimately viewed as far fetched" is not the same as "not feasible". "best effort to develop a conceptual model" is not anything like saying it's not feasible. Finally, from the link Robby provided, Koonin writes:

However, evolution of the coupled system of replication and translation does not appear possible without pre-existing efficient replication; hence a chicken-egg type paradox. The currently preferred solution is the concept of the RNA World which is conceived as a community of RNA molecules replicating without the help of proteins, with versatile catalytic activities including the replicase activity. However, despite considerable accumulated evidence of catalytic activities of RNA molecules, the RNA World concept encounters major hurdles and so far has offered no convincing scenarios for the origin of efficient replication and translation. I argue that the "many worlds in one" version of the cosmological model of eternal inflation implies that emergence of replication and translation by chance, as opposed to biological evolution, is a realistic possibility.

"major hurdles" and "so far has offered no convincing scenarios" are not the same as "not feasible". But more significantly, Koonin is arguing in favor of the chance arisal of a replication/translation system under a particular cosmological model. (I believe his cosmological thinking is confused, but that's another matter).

Robby · 10 October 2007

PvM:

What you scenario you think that Koonin believes does not matter nearly as much as what Koonin has stated that he believes. Did you read the two links I gave you? In one of them he directly states:

"However, despite considerable accumulated evidence of catalytic activities of RNA molecules, the RNA World concept encounters major hurdles and so far has offered no convincing scenarios for the origin of efficient replication and translation. I argue that the "many worlds in one" version of the cosmological model of eternal inflation implies that emergence of replication and translation by chance, AS OPPOSED TO BIOLOGICAL EVOLUTION, is a realistic possibility....
A major corollary of this scenario is that an RNA world, as it is currently conceived, might have never existed although catalytic activities of RNA were, probably, critical for the onset of biological evolution and its early stages."

(http://www-ctp.mit.edu/cosmo/y0607/koonin_abs.html)

Koonin states in his paper:

"All this is not to suggest that OORT is a problem of "irreducible complexity" and that the systems of replication and translation could not emerge by means of biological evolution. It remains possible that a compelling evolutionary scenario is eventually developed and, perhaps, validated experimentally. However, it is clear that OORT is not just the hardest problem in all of evolutionary biology but one that is qualitatively distinct from the rest. For all other problems, the basis of biological evolution, genome replication, is in place but, in the case of OORT, the emergence of this mechanism itself is the explanandum. Thus, it is of interest to consider radically different scenarios for OORT....Translation is thought to have evolved later via an unspecified or, at best, invented ad hoc selective process. As discussed in the preceding section, both the ribozyme-catalyzed replication and, especially, evolution of translation in the RNA world face formidable difficulties. The MWO model dramatically expands the interval on the axis of organizational complexity where the threshold can belong by making emergence of complexity attainable by chance...I suggest that such a possibility should be taken seriously, given the paradoxes of OORT. A central corollary to this hypothesis is that the RNA World, as it is currently pictured, i.e., a vast community of replicating RNA molecules possessing a variety of catalytic activities but no translation system and no genetically encoded proteins, might have never existed. Of course, as discussed below, this does not at all rule out the special importance of ribozymes in early biology, in particular, in the primordial translation system."

(http://www.biology-direct.com/content/2/1/15)

How is this logic different from ID logic? Koonin uses an argument from improbability based upon what we know about translation (not gaps in our understanding) to argue that such a system cannot be approached by Darwinian means. At any rate, one does not need to accept a new model in order to reject an old flawed one. One can just say that, for the time being, we do not know. I do admire Koonin for trying to look at the matter from opposite his own view point. I think IDers and neo-Darwinists would both do well to look at systems see if there is a reasonable explanation for them considering the other point of view.

So to sum up, Koonin is a poor example to use because he negates the very point you were using him to try to make. He thinks that a theory can be rejected because of improbability and that this points to other alternatives. He is tentative about this, though, as should IDers be about their own theory. But what was your argument again?

Popper's Ghost · 10 October 2007

I am not sure that Koonin is as good of an example for this as you think he is.

What you seem not to realize is that science is not based on argument from authority. It isn't Koonin, but rather the content of the Wolf/Koonin paper, that is at issue, content that you have not addressed.

Robby · 10 October 2007

Two corrections:

I meant for the last post to begin with the words..."What scenario..." not "What you scenario..."

Second, I am not trying to suggest that Koonin supports ID. I am saying that he rejects the gradual evolutionary process as insufficient and improbable (he directly said it was not a realistic possibility). He instead tries to explain the origin of life (like the fine tuning of physical constants) in terms of an infinite multiverse. In such a place the chance appearance of a replication-translation apparatus without Darwinian explanation is guaranteed. The point is that this theory is not testable in the way that you said Koonin so exquisitely tests theories. In fact, his evidence for this theory is that the standard one is extremely improbable and self-defeating. Koonin almost suggests (though he does not outright state) that in any universe capable of Darwinian evolution a system such as a replication-translation apparatus COULD NOT evolve, since the selective forces "are mysterious" and would appear to prevent the origination of such a system because no intermediates would be advantageous. You may quibble about that point; but the point that you say Koonin illustrates a man who outlines detailed, testable hypotheses before adhering to a theory is just wrong.

PvM · 10 October 2007

Robby, stick to the topic or your postings will be unpublished until a more suitable home can be found. Address Wolf and Koonin's scenario, feel free to include the fact that they themselves do point out many of the weaknesses in said scenario. Despite all the weaknesses, their paper shows how science proposes hypotheses. What does ID have to offer? The question is simple and straightforward. Accusing Koonin of doing the same as ID and stating that

Koonin uses an argument from improbability based upon what we know about translation (not gaps in our understanding) to argue that such a system cannot be approached by Darwinian means.

No credible scenarios, indeed. Not that such a system cannot be approached by Darwinian means, or evolutionary means (two different though overlapping concepts). Koonin's approach of multiple universes however is not mutually exclusive with science finding a scientific explanation for translation, a scenario of which was provided by Wolf and Koonin in the paper I am discussing here. I will discuss the other solution provided by Koonin in another posting soon. Remember that the choices for the origin of the genetic code: frozen accident, selection or stereochemistry provides at least three alternative pathways. So what is ID's explanation? If Koonin is right and multiverses is the solution then ID is out of luck as it cannot even use any probability argument. However, I am interested in Wolf and Koonin's scenario and how it compares to any ID hypothesis. Arguing, incorrectly, that Koonin is using the same arguments as ID, is not a very good way to defend ID. Look at the proposed hypothesis which is the topic and explain how ID intends to deal with scientific hypotheses? Would it present its own hypotheses? Or would it merely state: 'Not enough detail, thus design'?

Popper's Ghost · 10 October 2007

What you scenario you think that Koonin believes does not matter nearly as much as what Koonin has stated that he believes.

It does when you are misrepresenting what Koonin believes.

by chance, AS OPPOSED TO BIOLOGICAL EVOLUTION, is a realistic possibility

Is English your native language? All Koonin is saying here is that chance, distinct from biological evolution, is a realistic possibility. He is not saying that biological evolution isn't a realistic possibility. In fact, in the very next paragraph you quote, he states this explicitly:

All this is not to suggest that OORT is a problem of “irreducible complexity” and that the systems of replication and translation could not emerge by means of biological evolution. It remains possible that a compelling evolutionary scenario is eventually developed and, perhaps, validated experimentally.

Sheesh.

How is this logic different from ID logic?

In just about every way.

Koonin uses an argument from improbability based upon what we know about translation (not gaps in our understanding) to argue that such a system cannot be approached by Darwinian means.

He does no such thing, and does in fact approach it in that fashion in the paper PvM discusses: "Our main guide in constructing the models is the Darwinian Continuity Principle ...". Sheesh.

So to sum up, Koonin is a poor example to use because he negates the very point you were using him to try to make.

To sum up, you are a poor judge of these matters.

Popper's Ghost · 10 October 2007

I am saying that he rejects the gradual evolutionary process as insufficient and improbable (he directly said it was not a realistic possibility).

Even by your inept and erroneous misreading, he did not say that "directly".

You may quibble about that point; but the point that you say Koonin illustrates a man who outlines detailed, testable hypotheses before adhering to a theory is just wrong.

PvM's post is not about Koonin's qualities, but about how science is done. Sheesh.

Popper's Ghost · 10 October 2007

the point that you say Koonin illustrates a man who outlines detailed, testable hypotheses before adhering to a theory is just wrong.

Even compared to the rest of Robby's misrepresentations this seems extraordinary. Can anyone point me to where Pim said this? Koonin isn't even mentioned, other than to identify him as an author. Pim points to what the authors of this paper do in this paper in the process of doing science. Perhaps Koonin spends much of his time consulting his horoscope, consuming homeopathic remedies, and attending the Church of the Subgenius, but none of that would relevant.

David B. Benson · 10 October 2007

Off-topic, but I recently found a web site offering to sell T-shirts with various genuine bits of geology information on them. And one spoof:

Intelligent Plate Tectonics

raven · 10 October 2007

Since this thread ran down for the usual reason, I'll toss something in that is related to abiogenesis.

That is that life or the start thereof may have arisen elsewhere and been seeded here. This is panspermia, championed by Crick among others. When Crick first started talking about this, a lot of people, myself included thought he was getting a bit soft in the head.

But so what? It can't be excluded right now. This btw, doesn't necessarily require supernatural beings or intelligent aliens. We know some of the dust in the solar system is primordial and chunks of the moon and Mars have been found on earth.

For all we know, the local galactic neighborhood or the whole galaxy could be a DNA/RNA L-amino acid clade.

Popper's Ghost · 10 October 2007

This is panspermia, championed by Crick among others.

Crick? Back in the early '70s. But in 1993 he co-wrote Anticipating an RNA World Some Past Speculations on the Origin of Life: Where Are They Today?

Nick · 11 October 2007

Thanks, this paper is incredibly interesting.

And useful, hehehe, creo's will never know what hit them...

Frank J · 11 October 2007

Let’s see, I think the IDers believe (at least some of them, since nothing reliable is written down) in multiple “kinds” poofed during the “Precambrian Explosion” with subsequent micro-evolution.
— MemeticBottleneck

That, assuming you mean of separate origin-of-life events for each "kind", seems to be what a typical ID argument leads most people to infer, but it's not necessarily what the promoter believes. Michael Behe has stated for years that he accepts common descent, which means that he disagrees with that scenario. But no other major IDer has ever publicly disagreed with him. Note also that, unlike YECs and OECs, IDers usually leave out when those events occurred (though when they do say "when" they agree with "progressive" OECs). That, and many other tactics of ID scammers tells me that, privately, they know that mainstream science is correct, and that none of the mutually contradictory creationist accounts are supportable by evidence. Yet their "don't ask, don't tell" approach allows sympathetic audiences to infer whatever creationist account they are comfortable with - without being distracted by its own scientific failure and irreconcilable differences with other accounts.

Popper's Ghost · 11 October 2007

Michael Behe has stated for years that he accepts common descent, which means that he disagrees with that scenario. But no other major IDer has ever publicly disagreed with him.

Huh? Dembski has denied common descent, and he's hardly the only IDiot to have done so; Behe is in the minority.

Popper's Ghost · 11 October 2007

And actually, even Behe's acceptance apparently isn't all that firm: http://jgrr.blogspot.com/2006/01/uncommon-descent-dont-dispute-common.html

Each witness was asked some version of this question: "Do you accept the general principle of common descent that all life is biologically related back to the beginning of life, yes or no?" The DI's Stephen Meyer: "I won't answer that question as a yes or no. I accept the idea of limited common descent. I am skeptical about universal common descent. I do not take it as a principle; it is a theory. And I think the evidence supporting the theory of universal common descent is weak." Angus Menuge: "Not as defined by neo-Darwinism, no." Nancy Bryson: "No." Ed Peltzer: "No." Russell Carlson: "No." Warren Nord: "I agree with limited common descent, but I don't believe in universal common descent because I don't see any scientific evidence for it, compelling evidence." Michael Behe: "My position is similar to Professor Nord's" Jonathan Wells: "Well, I stated in my power point that I find it extremely unlikely based on the evidence that the animal phyla are related through common ancestry. Other biologists have said they're dubious of common ancestry at levels higher than that. The levels in between, I don't know." Bruce Simat: "From the data that I've been following it's probably not true." Charles Thaxton: "Well, I have difficulty with common ancestry"

So what were you saying, Frank, about "no other major IDer"? I've noticed that you have a strong tendency to get things wrong -- you might want to go outside your own head and look at the evidence occasionally to see if it confirms your beliefs.

David Stanton · 11 October 2007

I wonder what the responses would be if we asked the same people if they think that the genetic code and transcription and translation mechanisms could have arisen by ordinary evolutionary processes. For those who responded no, I wonder if they would care to enlighten us as to exactly the the "designer" did and when. Probably not, since they never seem to enlighten us about what life forms were "designed" and "created" and when. It is very easy to ignore all of the evidence and then claim that that evidence did not convince you of anything.

Frank J · 11 October 2007

Huh? Dembski has denied common descent, and he’s hardly the only IDiot to have done so; Behe is in the minority.
— Popper's Ghost

First, most IDers will phrase it to keep their classic creationist fans (if not classic creationist leaders) happy. Second, no IDer has ever challenged Behe directly on common descent, even though that (open disagreement, as opposed to "big tent" silence) would only help their credibility with scientists. Third, AIUI, Dembski only said that he doubted that humans and other apes evolved from common ancestors; he did not rule out design-mediated "saltation" or "front-loading" that preserves Behe's "biological continuity." Fourth, don't forget that Dembski claimed that Carl Woese denied CD, which is not the case by any reasonable definition (note the frequent use of the "universal" qualifier). Last but far from least, you are assuming that these people are telling the truth.

Torbjörn Larsson, OM · 11 October 2007

An interesting paper to browse, that I will enjoy reading thoroughly later.

Especially since I now know not only of eigen values, but Eigen Cliffs. :-P it looks like Fig. 1 may illustrate a type of fold catastrophe that I have met before. By transformations the fold can start at the origin and scale linearly with the distance from it.

If a fold it will have an hysteresis, so when a system transitions from the lower manifold to the upper it will move to a stable position away from transitioning right back. Folds are nice as catastrophes go.

This work also pointed me to Koonin's "anthropic" papers. Seems Koonin has taken to the "a few solid papers, one speculative paper" approach so common among theoretical physicists. That can give some interesting ideas.

In any case, I may be in error since I have just browsed them yet but I think Koonin's cosmological thinking is confused (as PG notes).

The weak anthropic principle is used to predict values, successfully so for the cosmological constant and a few other parameters as of yet. It is not preferred as an open unfalsifiable "just so" description for finetunings or other low likelihood scenarios, as Koonin seems to propose.

Btw, it is ironical if biologists have started to use vacuum selection scenarios at this time. The earlier mutual support that inflation theory and string theory gave each other for vacuum selection may AFAIU have become problematic with some recent papers. And main stream physics has never taken to it, which of course doesn't mean it is wrong but that it isn't a strong contender as of now.

Torbjörn Larsson, OM · 11 October 2007

I could strengthen that. The weak AP is used to predict likely values, while Koonin seems to think it explains unlikely values (events).

MememicBottleneck · 11 October 2007

You guys can argue about what Behe believes until your keyboards wear out. It is unlikely that you'll ever get a straight clear answer from him. That, I believe, is by design :)

Like I said, I've never seen anything written down that codifies their "theory". Different ID'ers have different delusions. As soon as they define ID, too many people will start diving out from under the "big tent", because it will clash with their specific form of delusion.

Saying that design is whats left when you subtract everything that science has discovered, doesn't cut it. God of the gaps is bad science to begin with, but the DI goes one step worse. They will not define what they believe to be good or bad science. This, IMHO is because all science that clashes with the bible is "bad science", and will eventually need to be gotten rid of. I know what Behe said about the age of the earth in Dover, but does the DI preach this as part to the "theory" to the YECs. ID and all other forms of creationism deny science at various levels.

Maybe we could ask Mats or BJ Bond to pass on the secret observations of what constitutes good and bad scientific data to us. Maybe they could catagorize the different "kinds" from all the "research" that goes on at the Discovery Institute. Maybe hell will freeze over tomorrow.

Henry J · 11 October 2007

I wonder if they would care to enlighten us as to exactly the the “designer” did and when.

Some unspecified something did something unspecified at an unspecified time and unspecified place. Next question? :p

Popper's Ghost · 11 October 2007

Fourth, don’t forget that Dembski claimed that Carl Woese denied CD, which is not the case by any reasonable definition (note the frequent use of the “universal” qualifier).

That Dembski claims it supports the view that Dembski denies CD. That Dembski misrepresents Woese doesn't alter Dembski's denial of CD.

Last but far from least, you are assuming that these people are telling the truth.

I never assumed any such thing; as I said, you have a strong tendency to get things wrong.

Popper's Ghost · 12 October 2007

That Dembski claims it supports the view that Dembski denies CD

Hmm, even I had trouble parsing that. That Demsbki claims that Woese denied CD supports the view that Dembski denies CD.

Nigel D · 12 October 2007

I fail to see the logical connection.

Frank J · 12 October 2007

PG:

Last I heard Woese denied only that archaea and eubacteria are directly descended from a common ancestor. If that's the definition of CD, then I too might have some "difficulty," to use Thaxton's words.

Forgive me if it wasn't you, but this seems to be a deja vu of the thread a few months ago about how well IDers "understand" evolution. That, plus what they personally believe, is what I "get wrong" according to most people. But when you (or someone) qualified it as "misunderstand or pretend to," I was in complete agreement; I just like to emphasize the "or pretend to" part that almost everyone leaves out. No, I don’t think that ID leaders understand evolution as well as the top researchers in the field, but they certainly know the concepts and definitions better than most non-biologists, and more importantly, know how and when to bait-and-switch terms and concepts. So they probably understand a lot more than what comes across in their misrepresentations. Similarly for what they personally deny vs. what they lead others to deny. Besides, they have a great motive for pretending to misunderstand this and deny that.

Popper's Ghost · 12 October 2007

I fail to see the logical connection.

Really? You think IDiots quote mine "evilolutionists" for pure fun, rather than to support their positions?

Last I heard Woese denied only that archaea and eubacteria are directly descended from a common ancestor.

The issue is Dembski's (stated, not actually held) position. It doesn't matter what Woese denied, only what Dembski claims he denied. As I already said, "That Dembski misrepresents Woese doesn’t alter Dembski’s denial of CD." Your repeating irrelevancies and changing the subject does not impress me. You claimed that "no other major IDer has ever publicly disagreed with him" -- the claim was false. You then moved the goalposts to "no IDer has ever challenged Behe directly". No, they don't stand up and say "Michael Behe is wrong", but they do make statements that contradict his. Yes, I wrote "“misunderstand or pretend to”, but your "complete agreement" isn't with me, because I didn't claim that they pretend to, I merely provided it as a possibility. I think it's possible that some of them understand things that they pretend not to, and they certainly engage in some intentional misrepresentation of what we say, but I've spent a lot of time debating with these people and reading their work and I believe that it is wrong, and badly so, to think that it's all a sham, that they really believe in evolution and common descent but are pretending not to. I think that's a gross misunderstanding of their religion-spawned psychology and rather ignorant about the sorts of debates that have occurred between, say, ERV and Behe, or Elsbury and Dembski, as well as all the fisking that PvM has done here at PT of ID arguments. The IDiots would have to be pointlessly industrious in the extreme to produce so many arguments that largely go over the heads of their flocks just to give us material to shoot down. Dembski really does believe in his CSI and NFL arguments, and Behe really does believe in his IC arguments, despite the immense amount of intellectual dishonesty and cloudy thinking that is required to maintain those beliefs. And pointing to the Straussians Kristol and Himmelfarb is a huge mistake -- most IDiots really are ignorant, confused, and mentally challenged, and are not acting out some Straussian campaign of restricting true knowledge to the elites. But I don't really think there's much I can say that would sway you from views that, I believe, result from rather poor judgment.

Popper's Ghost · 12 October 2007

BTW, from that Reason article (which I have read more than once in the past), Unlike Berlinski, Behe more or less concedes that Darwinian evolution occurred once the biochemical systems operating inside of cells were "designed." Indeed, Berlinski has strongly challenged evolution and common descent; see, e.g., http://www.rtis.com/nat/user/elsberry/evobio/evc/biid/biidtdd.html

Frank J · 12 October 2007

Dembski really does believe in his CSI and NFL arguments, and Behe really does believe in his IC arguments, despite the immense amount of intellectual dishonesty and cloudy thinking that is required to maintain those beliefs.
— Popper's Ghost

Though I could be wrong about that too, I don't doubt that they truly believe that there's "informational discontinuity." That's because they are always willing to discuss it - or change the subject to it when they are asked specifically whether they deny "biological continuity."

Robby · 12 October 2007

PvM and Pooper’s Ghost:

Since you have invited me to challenge what you describe as Wolf and Koonin’s detailed scientific hypothesis (indeed, a hypothesis so detailed that IDers should aspire to its level of scientific rigor), let me see what I can come up with. I’ll begin by summing up their ‘detailed’ scenario (along with the assumptions and problems they set out to solve) as presented in their paper, and then make a list of points to consider.

I. A. Wolf and Koonin plainly attempt to address the seemingly paradoxical evolutionary transition from an RNA world to translation. The problem is that protein evolution would depend upon accurate coded translation, but accurate coded translation can only be achieved with fast acting, diverse and presumably highly evolved proteins. It is a chicken-egg type dilemma. The authors correctly state that selection for a translation apparatus before it could be useful (in terms of protein synthesis and evolution) is not feasible. So an exaptation route, one in which the system originally evolved for some other function and gradually acquired a new one, must be proposed. Wolf and Koonin note two additional subparadoxes below the main paradox that any exaptation route much address:
---From comparative analysis it has been determined that many proteins central to the translation process (such as translation factors and aminoacyl tRNA synthetases) are highly evolved (and are not even the earliest proteins), and so could not have played a central part in the original translation apparatus. For substantial protein evolution before and leading to these proteins, therefore, it is postulated that an RNA-only based translation machine (absent any proteins) was used. This apparatus must have been within an order of magnitude of accuracy of the present system in order for substantial protein evolution to occur. So the original system must have been fast and accurate based solely on RNA.
---From comparative analysis it has been determined that all tRNAs share a common ancestor and that they were derived from duplication and divergence. But there is a paradox here: “if, at some point in evolution, there was a single progenitor to tRNAs of all specificities, how could a translation system function – and, if there was no translation system at that stage, what would be the driving force of evolution of the amino-acid-specific tRNAs?”

B. Koonin and Wolf then make some assumptions about what an explanation must involve if they use the principle of continuity—that is a slow, gradual accumulation of function leading to translation without strained improbable steps. There assumptions are:
1. The Principle of Continuity
2. RNA world with versatile function including replication preceding translation
3. Evolution has no foresight
4. Comparable fidelity of translation in the RNA world as in the modern protein dominated apparatus
5. Interactions or lack thereof of amino acids with codons and anticodons
6. Direct templating of amino acids on messenger sequences is stereochemically implausible, so adaptors are necessary from the beginning
7. Compartmentalized ensemble of selfish replicating RNAs
8. Ready formation of nontemplated peptides by ribozymes

C. Koonin and Wolf’s explanation involves these basic steps:
0. Ribozyme (Rib1) catalyzes arbitrary X  Y reaction with selectable function.
1. Rib1 binds free floating amino acid(s) that improve reaction, and selection favors the interaction, preserving and improving it.
2. Rib1 gains the ability to join amino acids together in addition to its X Y reaction function. Peptide improves reaction and is preserved and optimized
3. A copy of Rib1 loses peptide when it decays and peptide attaches to a different ribozyme E, improves its catalysis, and interaction between E and peptide is preserved
4. Rib1 duplicates so that there is Rib1 and Rib2. Rib1 maintains original function X Y while Rib2 loses this function in favor of ligase activity because of selective pressure for peptide production. Selective pressure outweighs the replication cost of carrying multiple copies.
5. RNAs bind amino acids in cell to stifle their ready diffusibility for amino acid accumulation. These are proto tRNAs
6. tRNAs are diverse by duplication and divergence
7. Rib2 evolves the abilty to bind tRNA instead of individual amino acids and evolves transpeptidation ability.
8. Rib2 develops a subunit to specifically recognize tRNA for more efficient binding. This is a stage where coding and catalysis are still coupled.
9. tRNAs enter a bottleneck to common ancestor from which they are all derived.
10. Subunit M used for base pair complementarity separates from Rib2 and is used for coding and is not associated with catalytic activity. When M happens to code for useful or partially folded peptides, selection preserves the change and evolution takes off.
11. A ribosomal ratcheting mechanism is evolved when tRNAs separate from Rib2/subunit complex.

This is a rough and ready summary of Koonin’s hypothesis.

Now my comments…

II. 1. I first take issue with some of the basic assumptions of the paper. One of the first is that there was or could have been an RNA only translation machine antedating both LUCA and almost all protein folds that was comparable in terms of speed an accuracy to the modern system. The crux of the paper depends upon the ideal that protein evolution must have been guided by an accurate ribozyme translation system. But could any riboorganism even reach the threshold of complexity to code for an accurate system of translation, and if such a system is possible and comparable to the modern system in terms of fidelity and speed, what selective pressure drove proteins to replace ribozymes in the apparatus, since the two apparently functioned almost equivalently (by necessary assumption of Koonin and Wolf)? Koonin and Wolf rightly refer to Eigen’s paradox and Eors Szathmary’s work on relaxed error thresholds. Szathmary stated in the original paper http://www.colbud.hu/links/news/NaturGenet_2005press.pdf that with a fidelity rate of 0.999 (meaning an error rate of 10^-3), a genome of ~7000 nucleotides could be encoded. Koonin and Wolf state that, “Conceivably, this is, roughly, the intrinsic complexity limit on ensembles of co-evolving ‘selfish cooperators’ that might have been the ‘organisms’ of the RNA world.” Putting aside the fact that Szathmary’s results are generalized from specific results and may not be indicative of the error threshold for most replicators, would the max limit of an RNA genome complexity of 7000 nucleotides be enough to encode for the translation and metabolic functions expected of it? Keep in mind we are talking about the late RNA world, not the early RNA world. Late riboorganisms must have had substantial metabolic complexity in order to function, as they would deplete raw materials extracted from their environments (such as nucleotides and nucleotide derivatives, if they were even available at all). See http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=10359720&dopt=AbstractPlus Szathmary states in his paper that, “Such a ribozyme could replicate a genome of more than 100 genes each of sequence length 70 each…This would be sufficient to run a functionally rich riboorganism, estimated to carry about the same number of genes. A recent analysis of the core minimal bacterial gene set places the value at about 200 genes. If we take away genes encoding the whole contemporary translation system, we are in the same range.”
There are several things to think about in this quote. First, in order to get minimal bacterial gene requirements to match the maximum complexity of an RNA genome (since they are presumed to have had many of the same functions and pathways, with proteins supplanting RNA in later stages), THE ENTIRE SET OF GENES ENCODING TRANSLATION HAD TO BE TAKEN AWAY. But Koonin’s reasoning REQUIRES a riboorganism to encode a fairly accurate translation apparatus. You cannot take it away to make the two values equal one another, as Szathmary did. Szathmary also cites Poole et al who make an estimate that a complex riboorganism could get away with about the number of genes that Szathmary’s error rate permits. I have my doubts about this. Sydney Benner has stated that, “ ...one is forced to conclude that the last ribo-organism had a relatively complex metabolism that included oxidation and reduction reactions, aldol and Claison condensations, transmethylations, porphyrin biosynthesis, and an energy metabolism based on nucleoside phosphates, all catalyzed by riboenzymes.” One needs many requirements for a riboorganism, such as the biosynthetic pathways for all four nucleotides and lipid synthesis. It is not clear that these reactions can be carried out by ribozymes (since they have not all been demonstrated within ribozymatic catalytic capability), but so far the reactions that have been demonstrated require many ribozymes of considerable length. It is doubtful that a riboorganism with all the metabolic and translation complexity required of it could be sustained with 7000 nucleotides. (Just look at the dozens of long ribozymes scientists have had to study just to show that ribozymes can accomplish some of the functions of translation.) Second, a ribozyme replicase with an accuracy of 10^-3 has never been demonstrated in the laboratory, despite billions and trillions of RNAs with unreal selective pressure. It may not even be possible to achieve such a replicase. Robert Shapiro has noted:
“A very elaborate and discriminatory polymerase, with capabilities beyond those of any known protein or ribozyme polymerase, would be needed to accurately select the correct four activated nucleotides from this array… The above considerations permit the abiotic synthesis of a functional RNA replicator on the early Earth only as an extremely improbable event .” (http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16776061&ordinalpos=4&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum)
What would such a replicase look like, and how long would it be? What ribozymes would have to accompany it in order to function properly? What are the odds that these ribozymes would aggregate and cooperate properly in hydrothermal vents or the prebiotic sea?

Thus, there is very good reason to harbor considerable doubt as to the basic assumption of Koonin’s paper. And even granting Koonin’s assumption is true, why would a protein centered apparatus replace an RNA centered apparatus if they are functioning with the same speed and accuracy? What is the selectable difference?

2. The steps of Koonin and Wolf’s solution themselves are a far, far cry from a ‘detailed’ or ideal scientific hypothesis. They are postulating imaginary reactions that may or may not have a parallel in reality. In my opinion, they are too vague to test. As an example, look at this paper by Chen and Ellington http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17443876&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum

These authors list many ACTUAL reactions that would have had to been carried out by ribozymes in order to evolve a ribozyme translation system. These reactions include:
a. Acyl activation
b. Acyl-CoA synthesis
c. Hydroxy Group Acylation from Adenylate
d. Peptide Bond formation from Adenylate
e. Acyl Transfer between Thiol Groups
f. Hydroxy Group Acylation from a Thioester
g. Peptide Bond formation from a Thioester
h. Acyl Transfer Between Hydroxy Groups etc.

Many of these reactions have been mimicked by ribozymes, though not all. The interesting thing is that we must come up with a sequence by which these separate ribozymes catalyzing separate and necessary reactions interacted to produce a prototranslation apparatus. Koonin does not do this because he does not even consider real and required chemical reactions. All we have is “Rib1 catalyzes X  Y reaction.” What reaction? What was the selectable function? How did the ribozymes interact?

You call this a solid, detailed hypothesis? It doesn’t even approach explaining the complexity of translation.

3. But even considering the cartoon scenario created by Koonin and Wolf, there are still problems. In step 2, how plausible is it that two or more cofactors to Rib1 would bind in such close proximity that an oligopeptide would result? Is there a ready source of energy for this peptide ligase, and is such an energy source feasible? Why was it so that this peptide increased functionality or efficiency of the reaction instead of interfering with it? In step 4, why did selection favor copying both Rib1 and Rib2 instead of dispensing altogether with Rib2 for more efficient replication costs? We are, after all, talking about an ensemble of selfish replicators. This is especially important at the stage in which Rib2 was just a copy and had not yet elaborated its peptide ligase function. What about uncoupling coding from catalysis at steps 8 – 10? Is it very feasible that the coding sequence M and the ribosomal subunit originated from Rib2, like an Adam’s rib-type scenario for the origin of the mRNA? We do not have any detail at all and we do not know how likely each step is, or what sorts of chemical reactions each step involves. Koonin and Wolf admit this much, saying:

“The current scenario for the evolution of translation in the RNA World faces formidable difficulties because, although the ribozyme catalysis of the elementary reactions required for translation has been demonstrated experimentally (Table 1), the required complex RNA-mediated functions have not. The crux of the problem seems to lie in the postulated catalytic adaptors that would have to possess a notable spectrum of capabilities including, in addition to the apparently feasible specific recognition of amino acids and self-aminoacylation, the ordered binding to the progenitor of the large subunit (RL), and at a subsequent stage, recognition of a specific region in the progenitor of the small subunit (RS). With regard to RL and RS themselves, ribozyme stimulation by amino acids and peptides has been demonstrated but, beyond that, the postulated properties of these molecules remain hypothetical. It seems that a focused experimental effort aimed at the construction/selection of ribozymes with the properties of the postulated T RNAs, in particular, their postulated interaction with other, more complex ribozymes, could provide crucial evidence in support of this or a similar scenario for the evolution of translation.”
This whole mess is one long just so story. Why was it this way? Why was this so? It was so because it was just-so. That’s the answer. The path to translation was a long and grueling one, involving constructing several interdependent pathways of dozens of different ribozymes with different functions while replication fidelity was low. We have not even scratched the surface of a viable evolutionary explanation for this. All current exaptational scenarios are either vague or improbable or both. Koonin says this much himself in his cosmological paper when he states:

“Speculative scenarios have been developed on the basis of the idea that even short peptides could provide selective advantage to an evolving system in the RNA world by stabilizing RNA molecules, affecting their conformations or enhancing their catalytic activities [31-33] (see Ref. [34] for an attempt of a synthesis on this direction in the study of translation origins). These ideas are compatible with observed effects of peptides on ribozyme activity [35] but none of the scenarios is complete or supported by any specific evidence, and all include reactions without precedent in modern biological or model systems….Despite considerable experimental and theoretical effort, no compelling scenarios currently exist for the origin of replication and translation, the key processes that together comprise the core of biological systems and the apparent pre-requisite of biological evolution. The RNA World concept might offer the best chance for the resolution of this conundrum but so far cannot adequately account for the emergence of an efficient RNA replicase or the translation system.”

4. Maybe I missed something, but did Koonin ever resolve his second paradox with the common origin for all tRNAs? I will hold back on making any points about this, since I am not sure my reading of the text was accurate enough to comment on his failure or success in resolving the problem.

5. PvM stated that Koonins many world’s hypothesis was not at odds with finding an evolutionary explanation for translation. PvM, let me introduce you to Koonin. In his Cosmological paper he states:

“As soon as the possibility of biological evolution at a lower level of complexity, e.g., in the RNA world, is demonstrated and the route from the RNA world to the translation system is established, either experimentally or, at least, in a compelling model, the origin of a complex system with coupled replication and translation by chance/anthropic selection will be, effectively, ruled out.”

Koonin sets the two up as opposing worldview, and if a viable evolutionary model is demonstrated for translation he will abandon his views. There is no evidence for MWH other than the improbability and conceptual problems of current exaptation scenarios for the origin of life.

6. PvM notes the very detailed, step by step account proposed by Wolf and Koonin is exactly how ID should formulate their hypotheses. Does PvM realize that the reason why a detailed, step by step process is necessary is because the model ASSUMES THAT EVOLUTION HAS NO FORESIGHT AND NO TELEOLOGICAL OR GOAL-ORIENTING PRINCIPLES WERE GUIDING THE FORMATION OF THE TRANSLATION APPARATUS! If we assume that evolution does have foresight, then formulating the detailed, step by step scenario by which it was formed is both impossible and unnecessary. Which component came first, under a teleological model? Answer: it doesn’t matter. If the goal is kept in mind all during the process, then intermediate steps need not be functional, and so there are several ways of constructing the translation apparatus. The notion of a detailed, step-by-step scenario is self-defeating when applied to ID. This is not very satisfying, admittedly. I do not contest that point. But when you ask yourself why you would need a step by step mechanism, and the answer is that you need one in the absence of foresight, then why in the world would you apply the same criterion to a model that DOES include foresight?

Incidentally, I wonder how PvM would respond to this question: HOW COULD THE TRANSLATION APPARATUS BE CONSTRUCTED IN ORDER TO YIELD A DESIGN INFERENCE? It is a viable question, right? Is there any way that the apparatus could be put together that would make you think, ‘Oh, that was bioengineered!’ If you cannot come up with one, then what is the use of comparing ID to a neoDarwinian view of the origin of these systems? ID has been ruled out by default.

7. I seriously question Popper’s Ghost’s ability to read and comprehend Koonin, any of his works, or the English language in general. Beyond saying this, I will say no more. I’m sure Popper’s Ghost, wherever he is looming, perhaps in his mother’s basement or at the local video arcade, will have enough indecent comments for two.

I’ve spent way too much time responding to this post, and I intend to spend no more. Cheers.

Nigel D · 12 October 2007

I fail to see the logical connection.
— I

Really? You think IDiots quote mine “evilolutionists” for pure fun, rather than to support their positions?
— Poppers Ghost

I was not questioning your logic, PG, but the logic (or lack thereof) contained within your parsing of Dembski's claim, i.e. "that Demsbki claims that Woese denied CD supports the view that Dembski denies CD."

Nigel D · 12 October 2007

I first take issue with some of the basic assumptions of the paper. . . the first is that there was or could have been an RNA only translation machine antedating both LUCA and almost all protein folds that was comparable in terms of speed an accuracy to the modern system.

(My bolding) But we know of no system or law or mechanism that would firmly rule out such a possibility; ergo, we must consider it possible.

The crux of the paper depends upon the idea that protein evolution must have been guided by an accurate ribozyme translation system. But could any riboorganism even reach the threshold of complexity to code for an accurate system of translation,

What is the "threshold of complexity"? Why does there have to be a theshold, and how would you go about measuring that complexity?

and if such a system is possible and comparable to the modern system in terms of fidelity and speed, what selective pressure drove proteins to replace ribozymes in the apparatus, since the two apparently functioned almost equivalently (by necessary assumption of Koonin and Wolf)?

While ribozymes are indeed versatile, they cannot match the chemical versatility of proteins. As soon as the two systems existed, there would have been competition between them. Once proteins existed, it is possible that some kind of ribonuclease could have evolved. It is conceivable that the replacement of ribozymes by proteins in the translation apparatus was anecessary adjunct to the evolution of ribonucleases. Ribonucleases are advantageous for two reasons: (1) better control over gene expression, and (2) defence against RNA viruses. My feeling is that the first organism to have evolved an efficient protein-translation system would probably be a direct ancestor of the LUCA.

Popper's Ghost · 13 October 2007

Really? You think IDiots quote mine “evilolutionists” for pure fun, rather than to support their positions?

I was not questioning your logic, PG, but the logic (or lack thereof) contained within your parsing of Dembski’s claim, i.e. “that Demsbki claims that Woese denied CD supports the view that Dembski denies CD.” I can't make any sense of that; it's my claim, my inference, and I explained it: Dembski claims that Woese denies CD in support of Dembski's own denial of CD.

Popper's Ghost · 13 October 2007

Since you have invited me to challenge what you describe as Wolf and Koonin’s detailed scientific hypothesis

I didn't make any such invitation; rather, I pointed out numerous errors and misrepresentations on your part, none of which you have addressed; rather, you offer only a pathetic ad hominem -- hardly surprising.

Popper's Ghost · 13 October 2007

But we know of no system or law or mechanism that would firmly rule out such a possibility; ergo, we must consider it possible.

Indeed, the suggestion that a mere assumption of possibility needs to be defended reeks of agenda-driven intellectual dishonesty.

Popper's Ghost · 13 October 2007

PvM notes the very detailed, step by step account proposed by Wolf and Koonin is exactly how ID should formulate their hypotheses. Does PvM realize that the reason why a detailed, step by step process is necessary is because the model ASSUMES THAT EVOLUTION HAS NO FORESIGHT AND NO TELEOLOGICAL OR GOAL-ORIENTING PRINCIPLES WERE GUIDING THE FORMATION OF THE TRANSLATION APPARATUS! If we assume that evolution does have foresight, then formulating the detailed, step by step scenario by which it was formed is both impossible and unnecessary. Which component came first, under a teleological model? Answer: it doesn’t matter. If the goal is kept in mind all during the process, then intermediate steps need not be functional, and so there are several ways of constructing the translation apparatus. The notion of a detailed, step-by-step scenario is self-defeating when applied to ID. This is not very satisfying, admittedly. I do not contest that point. But when you ask yourself why you would need a step by step mechanism, and the answer is that you need one in the absence of foresight, then why in the world would you apply the same criterion to a model that DOES include foresight?

Yeah, if the "explanation" is "goddidit", there's no need for all that "pathetic level of detail". Spoken like a true IDiot who has no grasp of the scientific process. "But when you ask yourself why you would need a step by step mechanism, and the answer is that you need one in the absence of foresight" -- no, you need a step by step mechanism because science seeks mechanisms. When studying human behavior, we don't just say that people have foresight, so there's no need to understand why they do what they do. And of course we never assume that some process has "foresight", whatever that could mean. Foresight is an attribute of agents, not processes, and we never propose it when we haven't even established that there's an agent involved.

SWT · 13 October 2007

Robby: PvM notes the very detailed, step by step account proposed by Wolf and Koonin is exactly how ID should formulate their hypotheses. Does PvM realize that the reason why a detailed, step by step process is necessary is because the model ASSUMES THAT EVOLUTION HAS NO FORESIGHT AND NO TELEOLOGICAL OR GOAL-ORIENTING PRINCIPLES WERE GUIDING THE FORMATION OF THE TRANSLATION APPARATUS! If we assume that evolution does have foresight, then formulating the detailed, step by step scenario by which it was formed is both impossible and unnecessary. Which component came first, under a teleological model? Answer: it doesn’t matter. If the goal is kept in mind all during the process, then intermediate steps need not be functional, and so there are several ways of constructing the translation apparatus. The notion of a detailed, step-by-step scenario is self-defeating when applied to ID. This is not very satisfying, admittedly. I do not contest that point. But when you ask yourself why you would need a step by step mechanism, and the answer is that you need one in the absence of foresight, then why in the world would you apply the same criterion to a model that DOES include foresight?

Hmm ... I thought that ID's Explanatory Filter said that we conclude design when we've ruled out chance and regularity. So, by developing a mechanism that's based strictly on chance and regularity, they are doing exactly what ID methodology tells us to do, aren't they? In most fields, when investigators look at designed artifacts, they are very interested in how the artifacts were designed and manufactured, and by whom they were designed and manufactured. (Examples: Considerable effort has been expended figuring out how various ancient peoples manufactured flint axes and arrowheads and figuring out how the pyramids were constructed. When I worked in industry, I spent some time reverse engineering chemical processes used by competitors ... developing a step-by-step reconstruction of a designed process.) Why should biology stand alone in not investigating the process by which modern organisms appeared? If you start with the assumption that modern organisms, or certain features of modern organisms, are designed, aren't the obvious next questions "who" and "how"? How incurious do you have to be not to want answers to those obvious questions? Of course, starting with the assumption of design violates the algorithm of the explanatory filter, doesn't it?

PvM · 13 October 2007

PvM notes the very detailed, step by step account proposed by Wolf and Koonin is exactly how ID should formulate their hypotheses. Does PvM realize that the reason why a detailed, step by step process is necessary is because the model ASSUMES THAT EVOLUTION HAS NO FORESIGHT AND NO TELEOLOGICAL OR GOAL-ORIENTING PRINCIPLES WERE GUIDING THE FORMATION OF THE TRANSLATION APPARATUS!

Exactly, these are foundational principles which have guided scientists to propose their pathways. If ID has a better approach then surely they could apply their principles? Let me guess, ID states that the pathways were exactly the same as Wolf and Koonin outline but that there was a guiding mind?

PvM · 13 October 2007

I thank Robby for his fortright admission that ID cannot really provide any detailed answers.

PvM · 13 October 2007

2. The steps of Koonin and Wolf’s solution themselves are a far, far cry from a ‘detailed’ or ideal scientific hypothesis. They are postulating imaginary reactions that may or may not have a parallel in reality.
— Robby

Let's for the moment agree, so what does ID have to offer that at least meets what you consider to be a 'far cry from a detailed or ideal scientific hypothesis'?

6. PvM notes the very detailed, step by step account proposed by Wolf and Koonin is exactly how ID should formulate their hypotheses. Does PvM realize that the reason why a detailed, step by step process is necessary is because the model ASSUMES THAT EVOLUTION HAS NO FORESIGHT AND NO TELEOLOGICAL OR GOAL-ORIENTING PRINCIPLES WERE GUIDING THE FORMATION OF THE TRANSLATION APPARATUS! If we assume that evolution does have foresight, then formulating the detailed, step by step scenario by which it was formed is both impossible and unnecessary. Which component came first, under a teleological model? Answer: it doesn’t matter. If the goal is kept in mind all during the process, then intermediate steps need not be functional, and so there are several ways of constructing the translation apparatus. The notion of a detailed, step-by-step scenario is self-defeating when applied to ID. This is not very satisfying, admittedly. I do not contest that point. But when you ask yourself why you would need a step by step mechanism, and the answer is that you need one in the absence of foresight, then why in the world would you apply the same criterion to a model that DOES include foresight? Incidentally, I wonder how PvM would respond to this question: HOW COULD THE TRANSLATION APPARATUS BE CONSTRUCTED IN ORDER TO YIELD A DESIGN INFERENCE? It is a viable question, right? Is there any way that the apparatus could be put together that would make you think, ‘Oh, that was bioengineered!’ If you cannot come up with one, then what is the use of comparing ID to a neoDarwinian view of the origin of these systems? ID has been ruled out by default.
— Robby

The inability of me or other ID proponents is just an indication that ID a posteriori fails. It's not that ID is ruled out, it's that scientists and ID proponents have come to agree that there is no scientific ID hypothesis. I understand why you follow Dembski's 'pathetic' approach and reject that ID should be held to scientific standards, which is exactly why ID is scientifically without merrit as it cannot and refuses to provide any scientific hypothesis beyond "I am not convinced, thus designed' Poof... So what do you think ID means by 'designed'? Hint, it has little relevance to what you may have come to believe Intelligent Design is all about.

PvM · 13 October 2007

It seems that Robby has found Dembski's "pathetic response" to a question by someone who wanted ID to provide a similar level of detail as science has provided.

As for your example, I’m not going to take the bait. You’re asking me to play a game: “Provide as much detail in terms of possible causal mechanisms for your ID position as I do for my Darwinian position.” ID is not a mechanistic theory, and it’s not ID’s task to match your pathetic level of detail in telling mechanistic stories. If ID is correct and an intelligence is responsible and indispensable for certain structures, then it makes no sense to try to ape your method of connecting the dots. True, there may be dots to be connected. But there may also be fundamental discontinuities, and with IC systems that is what ID is discovering.”
— Dembski

Nothing, nothing at all and yet ID pretends to be scientifically relevant, indispensable or even a scientific alternative. But all it is, is a position of ignorance camouflaged as 'design'. This was in response to a requestion by Rafe Gutman to

n regards to paul nelson's request for a description of an IC system's evolution, i believe i have provided a simple one for the complement system. i'll repost it in case you didn't notice it: the original complement protein contained a thioester group that is cleaved by serine proteases. when an infectious agent's serine proteases cleaves this protein, it exposes the thioester group, which then binds covalently to the pathogen's serine protease, inactivating it. later, the system evolved it's own serine protease (perhaps co-opted from the blood-clotting cascade), and could activate the complement protein by itself. now the system could protect itself from pathogens by attaching large amounts of complement to them, neutralizing them (agglutination). later, receptors appeared that facilitated the elimination of these complement-bound pathogens by phagocytosis (opsonization). later, the complement proteins evolved the ability to induce local inflammation (anaphylatoxins). finally, the complement system evolved a cytolytic ability (lysis). all of this proceeded through the mechanisms that yersinia initially described.

admittedly, i left out a lot of details, but if you want more, you'll first have to propose a model for the origin of an IC system through intelligent design in at least as much detail as i presented. that shouldn't be too hard, it's only 8 sentences. If ID cannot even meet this simple challenge, what is ID all about? Dembski seems to argue that ID is all about discontinuities (read ignorance). What do you believe?

PvM · 13 October 2007

5. PvM stated that Koonins many world’s hypothesis was not at odds with finding an evolutionary explanation for translation. PvM, let me introduce you to Koonin. In his Cosmological paper he states:

What Koonin is doing is showing regularity and chance, or chance alone hypotheses to explain the origin of the translation system, therefore exploring the range of solutions under the ID 'thesis'. Under the chance alone multiverse hypothesis, ID remains fully irrelevant, under the scientific pathway explanation paper, ID can still play a role by providing a similarly detailed explanation. Robby has shown that ID under either scenario seems to fail.

Popper's Ghost · 13 October 2007

I thank Robby for his fortright admission that ID cannot really provide any detailed answers.

He doesn't admit that it cannot, but claims that it doesn't have to ... because "we assume that evolution does have foresight". But that's what ID is supposed to demonstrate. Robby has admitted that ID is a scientifically vacuous circular argument. It claims that there is an intelligent designer at work. What justifies the claim? It was assumed! Robby says "This is not very satisfying, admittedly. I do not contest that point." Yes, it's not very satisfying, because it's not science. Science satisfies by finding out things, not by assuming them.

Incidentally, I wonder how PvM would respond to this question: HOW COULD THE TRANSLATION APPARATUS BE CONSTRUCTED IN ORDER TO YIELD A DESIGN INFERENCE? It is a viable question, right? Is there any way that the apparatus could be put together that would make you think, ‘Oh, that was bioengineered!’ If you cannot come up with one, then what is the use of comparing ID to a neoDarwinian view of the origin of these systems? ID has been ruled out by default.

No, Robby the IDiot, it would have been ruled out by its failure to be testable. If you and your IDiot buddies cannot come up with reliable criteria to distinguish designed from not designed, then ID isn't science. That's why Dembski tries to do so, but he has failed miserably. As for thinking "Oh, that was bioengineered!", who the hell (other than IDiots) cares what anyone thinks? Do you think that science journals are full of testimonials as to what impressions scientists have? But that is what ID is about -- its goal is to get people to think "Oh, that was intelligently designed!" Why? Because it's a religious enterprise that seeks converts.

Popper's Ghost · 13 October 2007

. I seriously question Popper’s Ghost’s ability to read and comprehend Koonin, any of his works, or the English language in general. Beyond saying this, I will say no more. I’m sure Popper’s Ghost, wherever he is looming, perhaps in his mother’s basement or at the local video arcade, will have enough indecent comments for two.

Of course you won't say more about my fisking that showed how you thoroughly misrepresented Koonin (and Pim) other than your childish ad hominem, because you're an intellectually dishonest fuckhead. My "indecency" is nothing compared to the indecency of the dishonest campaigns that you IDiot scum wage.

Popper's Ghost · 13 October 2007

5. PvM stated that Koonins many world’s hypothesis was not at odds with finding an evolutionary explanation for translation. PvM, let me introduce you to Koonin. In his Cosmological paper he states: “As soon as the possibility of biological evolution at a lower level of complexity, e.g., in the RNA world, is demonstrated and the route from the RNA world to the translation system is established, either experimentally or, at least, in a compelling model, the origin of a complex system with coupled replication and translation by chance/anthropic selection will be, effectively, ruled out.” Koonin sets the two up as opposing worldview, and if a viable evolutionary model is demonstrated for translation he will abandon his views.

This is an absurdly erroneous misinterpretation of what Koonin is saying. He wrote, before the quote mine, that his hypothesis, not "worldview", that the replication+translation system came about by chance is falsifiable, and then explained what would falsify it. Of course he would abandon a hypothesis once it is falsified. But the hypothesis of chance occurrence of this system is not the same thing as the cosmological model -- duh. He proposed that the cosmological model is one in which the chance occurrence is plausible, but ruling out chance occurrence of some event under a particular cosmological model doesn't rule out the cosmological model. Sheesh.

Popper's Ghost · 13 October 2007

If we assume that evolution does have foresight, then formulating the detailed, step by step scenario by which it was formed is both impossible and unnecessary.

In other words, if we assume that gardens are the result of fairies, it's impossible and unnecessary to provide a detailed explanation of their growth. (Of course, it would be possible simply by dropping the assumption.)

why in the world would you apply the same criterion to a model that DOES include foresight?

Robby's right; we shouldn't ask that ID explain biological phenomena, because ID is a fairy tale, not science.

Robby · 13 October 2007

My my my. It seems that I have attracted one or two serious commenters along with the pestering fly that is Popper's Ghost. What a lucky man am I.

First, the serious commenters. Nigel asks why there has to be a threshold of complexity for a riboorganism, how it is measured and what it is. May I direct him to the article I cited in my rebuttal by Eors Szathmary. It has to do with Manfred Eigen's mathematical insight on the limits of an error threshold that relates fidelity of replication to genome size. Szathmary's work suggests that our best estimates of an upper level complexity limit for an RNA organism, a replication fidelity of 0.999, is 7000 nucleotides. I pointed out that Koonin, who cited the paper and approved of this complexity limit, built a scenario around an RNA organism that must have encoded an accurate translation apparatus. I said that I doubted that 7000 nucleotides would be enough to encode for all the functions expected of the last riboorganism. Poole et al http://www.springerlink.com/content/q9q3ak4f1a30trf2/ estimate a minimum of 10,000 to 15,000 nucleotides for a riboorganism with all the functions expected of it. And that is a very generous estimate, considering that they had no estimate for many of the functions (since they haven't yet been demonstrated) and were uncertain about some of the functions that have been demonstrated (like nucleotide synthesis and fabrication). Not only this, but there have been studies mitigating against Szathmary's relaxed threshold. (See http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1774997, where authors state, "Although computer simulations show that compensatory and phenotypically neutral mutations can relax the error threshold for larger populations (tens of thousands) of catalytic RNAs (Kun et al. 2005), our experimental results show that small populations would still be at risk for accumulation of sublethal mutations. It is likely, then, that recombination would have been needed early in the history of life—even before the advent of cellular life and true sexual reproduction—as a means to maintain high-fitness genotypes.")

Also, no RNA based replicase has ever been observed, in the laboratory or otherwise, and none that would have the 10^-3 capability required for the 7000 nt complexity limit. Robert Shapiro doubts that such a replicase can exist, as I cited in my above reply, and gives several reasons. Worth a look.

So yes, it may not even be possible that Koonin's scenario could work because the assumption that his model is based on may be impossible considering Eigen's paradox. (We still do not know, but right now there is good reason to doubt.)

Moving on, PvM has stated that Koonin is exploring both the chance alone and chance + natural selction alternatives, but that they are both bad for ID because either way ID loses. May I bring it to PvM's attention that there is a logical possibility that he has overlooked: what if Koonin is right, and there are no compelling models for the origin of translation and so we must (Koonin's words)"consider radically different scenarios" for the origins of the system. But what if we have reason to doubt the many world's hypothesis? That leaves us in a position where there is one universe and in that universe the origin of such a system is highly improbable. Design /might/ be a possible explanation, right? It is not as if Koonin has somehow set up a foolproof system to lock out ID. It is not an either/or model. It could be that Koonin is right that the system itself is highly improbable (even considering Darwinian and exaptation routes) but that there are no universes other than this one. Where would we be then?

I have no problem with PvM stating that in historical sciences we look for intentions and motivations and processes of agents in making intelligently created artifacts. We should try to look for such motivations in biology as well, if we take inference to design seriously. But notice: THE DETAILS, MOTIVATIONS AND THE PROCESS BY WHICH AN ARTIFACT WAS CREATED ARE SOMETIMES INSCRUTABLE AND ARE DETACHED FROM THE INFERENCE TO DESIGN OF THE ARTIFACT. I have no idea how my car was assembled, who made the design, what order the parts were put together, what time, etc. I do know that it functions, and that someone designed it to function. My inference to design is not religious, and it doesn't depend upon the mechanism or process. It is commonsense. A purely mechanical explanation, devoid of agency, would depend upon, at least in a large degree (and to a larger degree than ID), the mechanism and details of the mechanism. Foresight makes the order and sequence a little harder to determine, since non-functional intermediates are allowed. Since non-functional intermediates are not allowed in a mechanical explanation, the step by step sequence, demonstrating functionality along the way, is much more important.

Where do I stand on Dembski's design filter? I doubt its validity. I don't think that he has formulated in an air-tight manner. But there has to be something to design. Look, it is a logical possibility, right? I mean, it is logically possible that agency can be responsible for bioengineering molecular machines. Just look at Sydney Benner's lab that is trying to build the genetic code based on an expanded genetic alphabet. So here is my (reformulated) hypothetical situation and question to you, PvM:

Say that a scientist, based on engineering principles, builds a novel molecular machine (or builds an existing one, such as the flagellar motor). Say that this scientist incorporates it in a bacteria, and sets it free into the wild. You find the organism, look at its structure, and decide to explain the molecular machine's origin. Are you going to reject the idea that the molecular machine was bioengineered out of hand? What if it was a bacterial flagella? Would you say that it was a sure thing evolution had built it? If you would, you would be wrong, even if you used the same line of reasoning that 'I cannot figure out how this machine was constructed by an agency, and until I do I must accept a natural explanation by default'. The inference to design cannot be a strictly religious, nonrational, nonscientific explanation.

Just so there is no confusion, I am all for getting detailed accounts for the intelligent origin of life. But if such explanations are not available, that doesn't derail the design inference, for the above reasons.

And now for the fly.

Popper's Ghost, my friend. I cannot decide what is funnier. The fact that you cannot read a scientific paper and the English therein or the fact that you have deluded into thinking that you have somehow given me an intellectual pounding. But what do I know. I'm just a 'fuckhead.' That made me laugh, so keep up the entertainment :)

You state

[quote] This is an absurdly erroneous misinterpretation of what Koonin is saying. He wrote, before the quote mine, that his hypothesis, not “worldview”, that the replication+translation system came about by chance is falsifiable, and then explained what would falsify it. Of course he would abandon a hypothesis once it is falsified. But the hypothesis of chance occurrence of this system is not the same thing as the cosmological model – duh. He proposed that the cosmological model is one in which the chance occurrence is plausible, but ruling out chance occurrence of some event under a particular cosmological model doesn’t rule out the cosmological model. Sheesh. [/quote]

Koonin said that the way to falsify his hypothesis is to show a credible evolutionary pathway, or that life on earth is shown not to be improbable by its presence elsewhere in the universe. Very similar to ID claims, since they too rely on the improbability of life and nonexistence of credible evolutionary explanations, don't you think And I quote...

"As soon as the possibility of biological evolution at a lower level of complexity, e.g., in the RNA world, is demonstrated and the route from the RNA world to the translation system is established, either experimentally or, at least, in a compelling model, the origin of a complex system with coupled replication and translation by chance/anthropic selection will be, effectively, ruled out. A demonstration that life independently emerged on several planets in our O-region will have the same effect."

On a related note, Koonin does indeed view the standard Darwinian and exaptation routes as implausible. He is open to such an explanation if one pops up (as IDers also claime), but he says that it is doubtful that such an explanation will ever arise, considering that this is a fundamentally distinct problem from the rest. He thinks that a radically new ideas need to be considered, and one of the only 'scientific' hypotheses around that square the improbability of life with its existence is an infinite universe or multiverse. There is no evidence for this conclusion other than that all the other scenarios are too improbable and that ID is unaccepatable. Let me quote Koonin directly, and let's see if you can read properly this time...

"...the solution sketched by Darwin centered around the evolutionary refinement of a primitive version of the function of the complex organ; subsequently, the importance of the exaptation route for the evolution of complex systems has been realized [18]. HOWEVER, ORIGION OF TRANSLATION RESISTS BOTH LINES OF REASONING. Primitive translation in a protein-free system is conceivable as an intermediate stage of evolution (see below) but this does not resolve the paradox because, even for that form of translation to function, the core components must have been in place already. Speculative scenarios have been developed on the basis of the idea that even short peptides could provide selective advantage to an evolving system in the RNA world by stabilizing RNA molecules, affecting their conformations or enhancing their catalytic activities [31-33] (see Ref. [34] for an attempt of a synthesis on this direction in the study of translation origins). These ideas are compatible with observed effects of peptides on ribozyme activity [35] but none of the scenarios is complete or supported by any specific evidence, and all include reactions without precedent in modern biological or model systems."

"It remains possible that a compelling evolutionary scenario is eventually developed and, perhaps, validated experimentally. HOWEVER, IT IS CLEAR THAT OORT IS NOT JUST THE HARDEST PROBLEM IN ALL OF EVOLUTIONARY BIOLOGY BUT ONE THAT IS QUALITATIVELY DISTINCT FROM THE REST....THUS, IT IS OF INTEREST TO CONSIDER RADICALLY DIFFERENT SCENARIOS FOR OORT."

"...Despite considerable experimental and theoretical effort, no compelling scenarios currently exist for the origin of replication and translation, the key processes that together comprise the core of biological systems and the apparent pre-requisite of biological evolution. The RNA World concept might offer the best chance for the resolution of this conundrum but so far cannot adequately account for the emergence of an efficient RNA replicase or the translation system.MWO version of the cosmological model of eternal inflation could suggest a way out of this conundrum because, in an infinite multiverse with a finite number of distinct macroscopic histories (each repeated an infinite number of times), emergence of even highly complex systems by chance is not just possible but inevitable."

"...I argue that the “many worlds in one” version of the cosmological model of eternal inflation implies that emergence of replication and translation by chance, as OPPOSED to biological evolution, is a realistic possibility."

Popper's Ghost, do you know what the word 'opposed' means? Do you know what the above statement means? It means that eternal inflation is a realistic possibility, CONTRARY OR OPPOSED TO EVOLUTION (meaning evolution is not). How do you escape the plain reading of Koonin and everything else he says? The man just doesn't buy the RNA world scenario, and until a model comes along, he is buying into internal inflation, not on the basis of evidence, but on the lack of evidence and conceptual hurdles involved in an RNA world.

Popper's Ghost, you incredibly dense, inane, pernicious little twit. You would do well to come off the 'theocracy conspiracy' that is being plotted by IDers and address the evidence that they give. No one here is trying to suppress atheists or evolutionists or anything of that sort. I certainly am not. I gave evidence for my propositions, and you haven't the intelligence to cobble together even a decent sounding reply. You are not worth the time I spend on you.

I gave up my vacation time to reply to this? Well, no more. I am done. Any further replies that you may make, consider them your victory. There is not more intelligent discussion to be had here.

PvM · 13 October 2007

Moving on, PvM has stated that Koonin is exploring both the chance alone and chance + natural selction alternatives, but that they are both bad for ID because either way ID loses. May I bring it to PvM’s attention that there is a logical possibility that he has overlooked: what if Koonin is right, and there are no compelling models for the origin of translation and so we must (Koonin’s words)”consider radically different scenarios” for the origins of the system. But what if we have reason to doubt the many world’s hypothesis? That leaves us in a position where there is one universe and in that universe the origin of such a system is highly improbable.
— Robby

That conclusion is begging the question. Given our current knowledge, the conclusion may be that pending new data, the origin of such a system is beyond our understanding. What if Koonin is right? Then we are left with a scenario of ignorance.

Design /might/ be a possible explanation, right? It is not as if Koonin has somehow set up a foolproof system to lock out ID. It is not an either/or model. It could be that Koonin is right that the system itself is highly improbable (even considering Darwinian and exaptation routes) but that there are no universes other than this one. Where would we be then?

Back at the drawing board. Of course, design can be a logical possibility but it has to compete with our ignorance and it cannot even do that.

I have no problem with PvM stating that in historical sciences we look for intentions and motivations and processes of agents in making intelligently created artifacts. We should try to look for such motivations in biology as well, if we take inference to design seriously. But notice: THE DETAILS, MOTIVATIONS AND THE PROCESS BY WHICH AN ARTIFACT WAS CREATED ARE SOMETIMES INSCRUTABLE AND ARE DETACHED FROM THE INFERENCE TO DESIGN OF THE ARTIFACT. I have no idea how my car was

I am amused by your ad hoc claim which mirrors ID's 'argument' but in fact, motivations, means, opportunity are essential when using an inference to design based on the approach chosen by ID and in fact, essential in many of the instances I have chosen to present.

assembled, who made the design, what order the parts were put together, what time, etc. I do know that it functions, and that someone designed it to function. My inference to design is not religious, and it doesn’t depend upon the mechanism or process. It is commonsense.

Common sense suggests a common sense as to how cars are being manufactured, what purpose they serve, an understanding of its history etc. Given a biological system with a function, ID attempts to use the function and our ignorance to suggest that ID is a better explanation. Better than our ignorance? ID cannot show that this is indeed the case without additional hypotheses.

A purely mechanical explanation, devoid of agency, would depend upon, at least in a large degree (and to a larger degree than ID), the mechanism and details of the mechanism.

But a mechanistical explanation is not devoid of agency.

Foresight makes the order and sequence a little harder to determine, since non-functional intermediates are allowed.

The same applies to biological evolution. So all we have is a process in which evolution provides scientific explanations, including near-neutral steps and ID which argues that because of foresight anything is possible and nothing constrained. That is not an explanation really.

Since non-functional intermediates are not allowed in a mechanical explanation, the step by step sequence, demonstrating functionality along the way, is much more important.

Yes, in ID it is sufficient to claim 'poof' allowing one to avoid providing ANY evidence, logic or pathways. All that is necessary is the empty statement that design is a logical plausibility. And science accepts this, however science also observes that ID presents no evidence, pathways, mechanisms, and hypotheses beyond calling something 'designed' because of our ignorance AND because it has function. How can something like this be called a scientific approach? Especially since materialistic explanations do allow for 'chance' or 'near neutral' processes and since materialistic processes does not preclude agency? Until IDers come to realize that materialistic processes nor science deny the logical plausibility of design nor deny the concept of agency. Once you shed that flawed assumption from ID, you come closer to its empty core.

PvM · 13 October 2007

Robby, you seem to consider Koonin's two papers, to be either/or arguments, in fact, a closer scrutiny suggests that Koonin has chosen two arguments to address the ID claims from a scientific perspective based on chance alone (multiverses) and/or the origin of the translation via natural processes of regularity and chance. The two papers are published in the same journal, in the same volume IIRC. But regardless, you have been tasked to show how ID explains the translation system, and your best answer is that asking ID to do this is unfair as such is not the nature of ID. But what does ID explain then?

Just so there is no confusion, I am all for getting detailed accounts for the intelligent origin of life. But if such explanations are not available, that doesn’t derail the design inference, for the above reasons.
— Robby

But it does since it makes the design inference incredibly unreliable and thus, according to Dembski, useless. If ID cannot logically avoid false positives, then it is useless. That there may be instances in which design is the correct explanation but science cannot find support for such a conclusion does not undermine the tentative nature of science. Science is more than happy to accept our ignorance, until a better explanation comes along. ID however provides no explanations.

Popper's Ghost · 13 October 2007

Popper’s Ghost, do you know what the word ‘opposed’ means? Do you know what the above statement means? It means that eternal inflation is a realistic possibility, CONTRARY OR OPPOSED TO EVOLUTION (meaning evolution is not).

No, you dishonest IDiot, it means that the subject of his assertion is one thing, not the other. He does not mean that evolution is not a realistic possibility -- clearly, because, as I already noted, he writes in the very next paragraph:

All this is not to suggest that OORT is a problem of “irreducible complexity” and that the systems of replication and translation could not emerge by means of biological evolution. It remains possible that a compelling evolutionary scenario is eventually developed and, perhaps, validated experimentally.

And he even co-authors a paper, the subject here, in which he explores that possibility.

I am done.

You said that before, jackass. We can only hope that you're telling the truth for once.

Popper's Ghost · 13 October 2007

I have no idea how my car was assembled, who made the design, what order the parts were put together, what time, etc. I do know that it functions, and that someone designed it to function. My inference to design is not religious, and it doesn’t depend upon the mechanism or process. It is commonsense.

But even you do not assume that the car production process is imbued with teleological principles and has foresight -- that would be foolish on several levels. So this is no argument in support of that assumption by IDiots. As for "common sense", in the case of the denial of evolution as a non-goal-seeking process, it's common ignorance. Your analogies fail, your logic fails, your parsing fails, so it's a commonsense conclusion that you're an idiot.

Popper's Ghost · 13 October 2007

Design /might/ be a possible explanation, right?

These IDiots just can't get it through their heads that "design" is not a member of the class "explanation". To phrase this non-IDiotically, "Design might possibly have had a causal role". Yes, and no one has ever denied it. But the possibility just sits there, doing nothing. It explains nothing, it tells us nothing, it doesn't further our understanding any, it isn't science.

Popper's Ghost · 13 October 2007

A purely mechanical explanation, devoid of agency, would depend upon, at least in a large degree (and to a larger degree than ID), the mechanism and details of the mechanism.

Ah, so just as IDiots are satisfied to say "goddidit", Robby is satisfied to know that his car was designed; the mechanism and details of the mechanism aren't of interest to him. What an IDiot. Robby also seems to think that cars come into being just by being designed -- the manufacturing process, being "a purely mechanical explanation", is apparently irrelevant. Here's news for Robby: even in the case of cars, which we know are designed by human beings, science does not consist simply of saying "cars are designed". It doesn't stop there; science not only explores every detail of the car mechanism and of its manufacture, it also explores every detail and mechanism of the designer. Human brains are not magical, they too have mechanistic explanations. Teleology only appears at the level of cognition, but vanishes into a cloud of cells and chemicals and physics below that. And in evolution, there is no cognition, so teleology doesn't apply there; cars are the result of goal seeking, flagella aren't -- common or not, that's what sense applied to the evidence tells us.

Popper's Ghost · 13 October 2007

A final note about Robby's incompetent campaign:

”…I argue that the “many worlds in one” version of the cosmological model of eternal inflation implies that emergence of replication and translation by chance, as OPPOSED to biological evolution, is a realistic possibility.”

can be translated into the clearer

…I argue that the “many worlds in one” version of the cosmological model of eternal inflation implies that it is a realistic possibility that replication and translation emerged by chance, as opposed to biological evolution.

But Robby, being the dishonest git he is, hinges an utterly bogus argument on an inept misreading of Koonin's non-optimal grammar -- a misreading sharply at odds with everything else Koonin wrote.

Torbjörn Larsson, OM · 15 October 2007

Well. I wish I had taken time to check up on this thread sooner, because Robby isn't your typical creationist. He is actually putting in some effort to understand the papers in question, and answer some of the questions on his critique.

(It would be even better if he had put in some effort to try to learn the science itself, for example by other than rhetorical questions. Alas, it was not to be.)

The main problems of Robby's analysis are aptly dealt with by PG, and the remaining details are too many for a dead discussion, but I would like to add an overview for posterity.

Koonin has presented a couple of speculative papers, which overlaps on the evolution of the DNA replication-translation machinery to give two different hypotheses. Robby uses details from the work of Koonin on one hypothesis as support to criticize details of Koonin's work on the other. But theories are ultimately judged on their successes or failures.

The paper that proposes a comprehensive model for the evolution of the DNA replication-translation machinery reduces the overall problem to a series of adaptive steps, making it amenable for tests under the current theory. Robby argues that the RNA world have problems, but as it is a reasonable assumption (independent support) it is outside the current model.

In fact, by showing that the DNA replication-translation machinery may plausible evolve, Koonin has strengthened the RNA world hypothesis. If his proposed evolutionary model is supported it would mean further support. It would also mean a new knowledge horizon to work further back from.

For all his work on his comments, I'm sorry to report that Robby displays the typical creationist reasoning. Whining about not considering untestable ID 'alternatives', using false choice (putting hypotheses against each other instead of against tests), and denying proposed tests ("This whole mess is one long just so story. ")

Finally, I can't abstain from noting that it is PG who does the logically correct reading of Koonin's claim (on "CONTRARY OR OPPOSED TO").

Popper's Ghost · 16 October 2007

Finally, I can’t abstain from noting that it is PG who does the logically correct reading of Koonin’s claim (on “CONTRARY OR OPPOSED TO”).

I wish that I had done the transformation I did at the end a lot sooner -- it's very hard to dismiss it as not even a possible interpretation. But the meaning is quite clear from the context, even if the language is slightly ambiguous. I pointed out more than once that Koonin's own language in the very next paragraph contradicted Robby's self-serving interpretation, and Robby always ignored the point, as he did throughout; over and over he repeated his misinterpretations while ignoring my direct quotes, instead launching a stream of juvenile ad hominem comments. Robby indeed isn't a typical creationist, but he shares their basic dishonest process that shields them from allowing anything in that challenges their crackpot views.

For all his work on his comments

Remember how much work Mark Hausam put in. It's always fascinating trying to understand these folks' psychology. Some, like Andre and Mats and BJB are relatively easy, but those like Mark and Robby are more challenging and interesting.

Popper's Ghost · 16 October 2007

Here's another point about the psychology of creationists: thinking logically is hard, and most human beings suck at it, even those who are reasonably intelligent like Robby. We see this at this site all the time, not just from the creationists but from commenters on "our side". One is additionally, terribly, handicapped if one is clinging to an erroneous conception like creationism or ID, because corrections by one's opponent to one's logical errors will seem to be mistakes by the opponent (especially if the opponent is as hostile as I am :-), whereas, if one is following the science, one's errors are corrected by one's "teammates" and thus are accepted and the errors are eliminated. So, scientists can get away with making errors without going far astray, but not creationists, who get further and further off track. And we can see this with Robby, where he makes logical error after logical error and not only has no mechanism to correct them but hardens when opposed by PvM and me. When I, who am (by numerous objective indicators) much better at reasoning logically, offer corrections, Robby hunkers down, doubts my ability to read Koonin (when it is his reading that is seriously flawed), says I am "incredibly dense" (despite my 170 IQ and remarkable clarity of thought according to some leading intellectuals), and disintegrates into a hail of misaimed insults. I'm sure that Robby really believes what he says and believes he's in the right and is mentally superior to me, but his beliefs are highly divergent from reality, lacking a corrective mechanism. If he ever recovers from his creationism, he may obtain that corrective mechanism and become relatively effective and productive, even with mediocre reasoning skills.

Mike · 20 October 2007

Quite apart from the whole ID politics, I have been on an Amazon board bemoaning the fact that there is no better advocate for ID to line up and flay. Especially all the ink they spend "flogging the flagellum" as I call it. Without knowing about this paper or this thread, I had already asked why one of them won't take shots based on the translation system as being irreducibly complex?

Robbie gets a nod from me for that effort.

Is ID science? No! Does it belong in public schools? No!

But even Wolf and Koonin swerve toward the metaphysical with that multiverse incorporaton to discuss biochemistry (obviously another universe can't be observed without being in it). As scientists they are able to be open to consider the spooky hardness of the problem and then just get on with the work.

I predict that someone will pick this up and write a book that will end up becoming the new ID text for Christian schools. This will not make the effort into science because it proposes nothing more than "poof", but it will be harder to dismiss as the flagellum was easier. Ultimately, it would serve to put the legal issues on a better footing because pulling the pseudoscience curtain back should be more obvious when even science itself understands the hardness of the problem and shows itself to confine it's search to testable physical reality. (Not that the courts so far have needed much pretext to laugh right at these silly kniggets.)

Torbjörn Larsson, OM · 20 October 2007

But even Wolf and Koonin swerve toward the metaphysical with that multiverse incorporaton to discuss biochemistry

Actually, I think it is Koonin's work alone that they refer to. He has published two speculative papers on the subject. I think he is misunderstanding why and how physicists are proposing (weak) anthropic selection. It is done to predict values of parameters with high likelihood. (As for example the successful prediction of the cosmological constant.) It is specifically not done to explain scenarios with low likelihood. And while multiverses and especially weak anthropic selection isn't especially popular among physicists we can't rule it out as of now. In fact, both the supported inflation mechanism and the hypothesized string theory have multiverses as natural solutions.

another universe can’t be observed without being in it

Not so. For a wide range of values of parameters we could possibly detect when other multiverses bump into ours. Even if this is a correct mechanism still the exact signature remains to be seen and tested. But that has of course not precluded people to jump the gun and speculate that certain features in the cosmic microwave background radiation is such a sign.

Torbjörn Larsson, OM · 20 October 2007

Oops. My concluding intention in the first part of the comment was to point out that multiverses aren't merely philosophical solutions at this time.

And maybe I should mention that I recognize the primary author on the detection paper, Anthony Aguirre, from other physics papers. It is a speculative paper and I haven't read it or seen any responses to it, but I a priori assume it is quite solid.

Mike · 24 October 2007

Torbjörn Larsson

Interesting. Thanks.
But perhaps you can explain the flaw in my reasoning: I say that by definition, anything that can be measured is part of the physical universe. If that happens to be in another brane or whatever, then the definition of universe needs amendment to include it? Can these other mutiverses have different physics or just different probability collapse?

The other thing I notice is that this seems to meet one of Radner & Radner's hallmarks of pseudoscience from "Science and Unreason": the "Anything is possible hypothesis". If there are an infinite number of universes, one for each possible outcome that does not violate conservation laws, however improbable, then somewhere every improbable thing will happen, such as the embedding of bogus dinosaur bones in strata or the development of a de-novo codon-anticodon transcription in a single step. This is hardly logically superior to special creation or intelligent design. It provides no basis in principle for discrimination between a miracle and an inevitability, and there is no payoff to developing causal explanations.

P.S.
That Radner and Radner book is great fun. (from the 80's)