Test of Cairns-Smith’s ‘crystals-as-genes’ hypothesis

Bullard, T. V.; Freudenthal, J.; Avagyan, Serine; Kahr, Bart

doi:10.1039/b616612c

Cited by 33 publications

(26 citation statements)

References 20 publications

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“…However, despite the greatest of care taken to not expose the fresh crystal seeds to atmosphere, and even in the absence of cleavage, new hillocks, "mutations" proliferated so that the detailed structure and morphology of the new crystals differed considerably from the original structure (116). We raise the question of whether they should be considered living entities.…”

Section: Are Cnp Live or Dead?mentioning

confidence: 94%

Pathological Calcification and Replicating Calcifying-Nanoparticles: General Approach and Correlation

Çiftçioğlu

McKay

2010

Pediatr Res

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Calcification, a phenomenon often regarded by pathologists little more than evidence of cell death, is becoming recognized to be important in the dynamics of a variety of diseases from which millions of beings suffer in all ages. In calcification, all that is needed for crystal formation to start is nidi (nuclei) and an environment of available dissolved components at or near saturation concentrations, along with the absence of inhibitors for crystal formation. Calcifying nanoparticles (CNP) are the first calcium phosphate mineral containing particles isolated from human blood and were detected in numerous pathologic calcification related diseases. Controversy and critical role of CNP as nidi and triggering factor in human pathologic calcification are discussed.

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Section: Are Cnp Live or Dead?mentioning

confidence: 94%

Pathological Calcification and Replicating Calcifying-Nanoparticles: General Approach and Correlation

Çiftçioğlu

McKay

2010

Pediatr Res

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“…The more general claim is that the RNA world comprised a stage of evolution preceding – perhaps immediately – the RNA/protein/DNA world we now inhabit. In this way, the hypothesis is not incompatible with models such as the ‘crystals-as-genes’ concept of Cairns-Smith [15], which proposes that the first replicators were imperfection-containing layers of clay that were able to pass on these imperfections to proceeding layers (unfortunately, one experimental test of Cairns-Smith’s model suggests that replicated defects are quickly overrun by random defects or noise [16]). Similarly, it has been hypothesized that RNA was preceded in evolution by a nucleic acid analogue – for example, one in which glycerol replaces ribose in the phosphodiester backbone – though pathways for the prebiotic synthesis of many such analogues are even less plausible than for RNA itself [17].…”

Section: Introductionmentioning

confidence: 99%

The RNA world hypothesis: the worst theory of the early evolution of life (except for all the others)a

2012

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The problems associated with the RNA world hypothesis are well known. In the following I discuss some of these difficulties, some of the alternative hypotheses that have been proposed, and some of the problems with these alternative models. From a biosynthetic – as well as, arguably, evolutionary – perspective, DNA is a modified RNA, and so the chicken-and-egg dilemma of “which came first?” boils down to a choice between RNA and protein. This is not just a question of cause and effect, but also one of statistical likelihood, as the chance of two such different types of macromolecule arising simultaneously would appear unlikely. The RNA world hypothesis is an example of a ‘top down’ (or should it be ‘present back’?) approach to early evolution: how can we simplify modern biological systems to give a plausible evolutionary pathway that preserves continuity of function? The discovery that RNA possesses catalytic ability provides a potential solution: a single macromolecule could have originally carried out both replication and catalysis. RNA – which constitutes the genome of RNA viruses, and catalyzes peptide synthesis on the ribosome – could have been both the chicken and the egg! However, the following objections have been raised to the RNA world hypothesis: (i) RNA is too complex a molecule to have arisen prebiotically; (ii) RNA is inherently unstable; (iii) catalysis is a relatively rare property of long RNA sequences only; and (iv) the catalytic repertoire of RNA is too limited. I will offer some possible responses to these objections in the light of work by our and other labs. Finally, I will critically discuss an alternative theory to the RNA world hypothesis known as ‘proteins first’, which holds that proteins either preceded RNA in evolution, or – at the very least – that proteins and RNA coevolved. I will argue that, while theoretically possible, such a hypothesis is probably unprovable, and that the RNA world hypothesis, although far from perfect or complete, is the best we currently have to help understand the backstory to contemporary biology.ReviewersThis article was reviewed by Eugene Koonin, Anthony Poole and Michael Yarus (nominated by Laura Landweber).

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“…While replication of chemical sequences through crystal growth has continued to be of interest (16) because of its simplicity and potential compatibility with a wide variety of chemistries, such replication has never been demonstrated. The replication of information in the form of crystal defects has been observed, but fidelity was very low (17).…”

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confidence: 99%

Robust self-replication of combinatorial information via crystal growth and scission

Schulman

Yurke²,

Winfree³

2012

Proc. Natl. Acad. Sci. U.S.A.

117

110

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Understanding how a simple chemical system can accurately replicate combinatorial information, such as a sequence, is an important question for both the study of life in the universe and for the development of evolutionary molecular design techniques. During biological sequence replication, a nucleic acid polymer serves as a template for the enzyme-catalyzed assembly of a complementary sequence. Enzymes then separate the template and complement before the next round of replication. Attempts to understand how replication could occur more simply, such as without enzymes, have largely focused on developing minimal versions of this replication process. Here we describe how a different mechanism, crystal growth and scission, can accurately replicate chemical sequences without enzymes. Crystal growth propagates a sequence of bits while mechanically-induced scission creates new growth fronts. Together, these processes exponentially increase the number of crystal sequences. In the system we describe, sequences are arrangements of DNA tile monomers within ribbon-shaped crystals. 99.98% of bits are copied correctly and 78% of 4-bit sequences are correct after two generations; roughly 40 sequence copies are made per growth front per generation. In principle, this process is accurate enough for 1,000-fold replication of 4-bit sequences with 50% yield, replication of longer sequences, and Darwinian evolution. We thus demonstrate that neither enzymes nor covalent bond formation are required for robust chemical sequence replication. The form of the replicated information is also compatible with the replication and evolution of a wide class of materials with precise nanoscale geometry such as plasmonic nanostructures or heterogeneous protein assemblies.algorithmic self-assembly | DNA nanotechnology | self-assembly I n cells, long genomes are accurately replicated via a complex replication process involving tens or sometimes hundreds of enzymes. Nearer to life's origins, a much simpler system must have been responsible for genome replication; evolution of this information then produced more and more complex forms. How a chemical system could be capable of sustained replication and evolution and yet be simple enough to arise spontaneously is an open question.Enzyme-free autocatalytic systems, which are generally simpler than those with enzymes, are known to exponentially replicate one or a small set of species (1-5), but none of these systems replicate an arrangement of subunits defining a combinatorial sequence of information. Without the capacity for combinatorial information replication, open-ended evolution, in which complexity increases without bound (6), cannot occur. Some RNA sequences have been shown to act as RNA polymerases that can assemble a general RNA sequence given a template (7). If such an RNA sequence polymerized a copy of itself, the required enzyme would be produced by the replication process, making it self-sustaining. However, fidelity sufficient for RNA-mediated RNA self-replication has not yet been observe...

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Test of Cairns-Smith’s ‘crystals-as-genes’ hypothesis

Cited by 33 publications

References 20 publications

Pathological Calcification and Replicating Calcifying-Nanoparticles: General Approach and Correlation

Pathological Calcification and Replicating Calcifying-Nanoparticles: General Approach and Correlation

The RNA world hypothesis: the worst theory of the early evolution of life (except for all the others)a

Robust self-replication of combinatorial information via crystal growth and scission

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