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Open Access

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

Biology Direct20127:23

DOI: 10.1186/1745-6150-7-23

Received: 9 May 2012

Accepted: 11 July 2012

Published: 13 July 2012

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.

This article was reviewed by Eugene Koonin, Anthony Poole and Michael Yarus (nominated by Laura Landweber).

RNA world hypothesis Proteins first Acidic pH tRNA introns Small ribozymes

The problems associated with the RNA world hypothesis are well known, not least to its proponents [1, 2]. In the following, I discuss some of these difficulties, some of the alternative hypotheses that have been proposed (including the ‘proteins first’ hypothesis), and some of the problems with these alternative models. As part of the discussion, I highlight the support provided to the RNA world concept by the discovery of some extremely small ribozymes. The activities of these provide support for proposals we have made previously for the identity of the first tRNA [3], for the origin of coded ribosomal protein synthesis [4], and for the evolution of an RNA world at acidic pH [5] (see also [6]). I also revisit the proposal for a replicase origin of the ribosome, and what has become the most commonly held model for the origin of tRNA.

In modern biological systems, the components of DNA are synthesized from RNA components [7], and it therefore makes sense to view DNA as a modified RNA. Similarly, the ribosome – the universal cellular machine that makes proteins – is composed mainly of RNA, and RNA is its active component, although there are indications that proteins may be playing an increasing role in some instances e.g.[8, 9] (even in the case of nonribosomal peptide synthesis [10, 11], the protein enzyme complexes that synthesize other proteins are of course themselves synthesized on the ribosome). RNA functions as both catalyst (e.g. in peptide synthesis and tRNA maturation) and genome (in RNA viruses such as HIV and influenza viruses). In contrast to nucleic acids, which associate according to the rules of base pair complementarity, the intricacies of protein structure do not – normally – allow for an easy mechanism of replication, which presumably explains the evolution of a coded system for their synthesis (for an interesting discussion of the contrasting molecular requirements for replication and catalysis, see [12]). Parsimony at least would seem to favour a scenario in which functions carried out by two classes of macromolecules in the modern system were, at an earlier stage, carried out by only one (for an alternative view however, see [13]). So which came first, the chicken or the egg? Protein or RNA? This is an underlying current in the debate surrounding the RNA world hypothesis, which I address when I discuss the ‘proteins first’ hypothesis.

Before beginning, it is important to clear up a common source of confusion. The RNA world hypothesis does not necessarily imply that RNA was the first replicating molecule to appear on the Earth (although a new paper by Benner and colleagues argues that this was, in fact, the case [14]). 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].

The following objections to the RNA world hypothesis have been raised:

RNA is too complex a molecule to have arisen prebiotically

RNA is an extremely complex molecule, with four different nitrogen-containing heterocycles hanging off a backbone of alternating phosphate and D-ribose groups joined by 3′,5′ linkages. Although there are a number of problems with its prebiotic synthesis, there are a few indications that these may not be insurmountable. Following on from the earlier work of Sanchez and Orgel [18], Powner, Sutherland and colleagues [19] have published a pathway for the synthesis of pyrimidine nucleotides utilizing plausibly prebiotic precursor molecules, albeit with the necessity of their timed delivery (this requirement for timed delivery has been criticized by Benner and colleagues [14], although most origin of life models invoke a succession of changing conditions, dealing as they do with the evolution of chemical systems over time; what is critical is the plausibility of the changes). A particularly interesting aspect of the pathway is the use of UV light as a method of isolating the naturally occurring nucleotides [18, 19], suggesting a possible means of nucleotide selection (see also [20]).

Although RNA is constructed with uniform 3′,5-linked backbones, recent work by Szostak and colleagues has demonstrated that ribozymes and RNA aptamers retain partial function when the standard 3′,5′-linkages are replaced with a mixture of 3′,5′- and 2′,5′- linkages, suggesting that a degree of heterogeneity may be compatible with (or even beneficial to) RNA function and synthesis (J. Szostak, pers. commun.; [21]). This complements an earlier study by Ertem and Ferris [22] that showed that poly C oligonucleotides with mixed 3′,5′- and 2′,5′-linkages are able to serve as templates for the synthesis of poly G oligonucleotides by nonenzymatic replication. Such work suggests that ancestral systems may not have been as tightly constrained as they are today.

Due perhaps to the molecular complexity of nucleic acids, metabolism-first models (as opposed to replication-first models such as the RNA world hypothesis) highlight the importance of the initial generation of small molecules through chemical or metabolic cycles. Establishment of a plausible energy source is a critical aspect of these models, some of which propose that life arose in the vicinity of hot alkaline (pH 9–11) under-sea hydrothermal vents, with energy provided by pH and temperature gradients between the vent and the cooler, more acidic ocean [2326]. In some ways, metabolism-first models appear not to conflict with the RNA world hypothesis, as they potentially offer a solution to the difficulty of ribonucleotide and RNA synthesis. A large point of difference, however, comes with the claim that such nucleic acid-free systems are capable of Darwinian evolution. Addressing this claim, Vasas et al.[27] have reported a lack of evolvability in such systems, while Benner and colleagues have noted the lack of experimental support from specific chemical models [14]. A more recent paper by Vasas et al.[28], while seemingly contradicting their earlier paper, uses a computational modeling approach without reference to a real-world chemical system (something noted by two of the reviewers in their published reviews).

RNA is inherently unstable

RNA is often considered too unstable to have accumulated in the prebiotic environment. RNA is particularly labile at moderate to high temperatures, and thus a number of groups have proposed the RNA world may have evolved on ice, possibly in the eutectic phase (a liquid phase within the ice solid) [2933]. Two of these studies [31, 32] demonstrated maximal ribozymic activity at −7 to −8°C, possibly due to the combined effects of increased RNA concentration and lowered water activity. A possible difficulty with this scenario is that RNA sequences have an increased tendency to base pair at such temperatures, leading in some cases to the formation of intermolecular complexes [34] that potentially could reduce catalytic activity.

A further problem is the susceptibility of RNA to base-catalyzed hydrolysis at pH >6 [35]. The phosphodiester bonds of the RNA backbone and the ester bond between tRNAs and amino acids – something similar to which would have been critical for the evolution of ribosomal protein synthesis – are both more stable at pH 4–5 [5, 6]. With our proposal for RNA world evolution at acidic pH [5], we have suggested that the primordial ‘soup’ may have been more like vinaigrette, while Hanczyc [36] has drawn a comparison with mayonnaise, with its emulsified mixture of oil in water (in light of these, could there be potential for food science to provide insights for origin of life studies?) While Mg2+ is important for stabilizing RNA secondary and tertiary structure, high Mg2+ concentrations also catalyze RNA degradation, which has been identified as a particular problem in the case of RNA template copying [21]. Here too, acidic pH offers a possible solution, as the positive charge on protonated cytosine and adenosine residues in acidic conditions may reduce the requirement for divalent cations. For example, a self-cleaving ribozyme with maximum activity at pH 4 isolated by in vitro selection, is active in the absence of divalent ions (including Mg2+) [37]. RNA secondary (and tertiary) structure would appear to be compatible with the presence of protonated nucleotides, as we have found an increased number of potentially protonated A-C base pair ‘mismatches’ in the tRNAs from acidophilic archaeal species with reported cytoplasmic pHs of 4.6-6.2 [5].

Catalysis is a relatively rare property of long RNA sequences only

The RNA world hypothesis has been criticized because of the belief that long RNA sequences are needed for catalytic activity, and for the enormous numbers of randomized sequences required to isolate catalytic and binding functions using in vitro selection. For example, the best ribozyme replicase created so far – able to replicate an impressive 95-nucleotide stretch of RNA – is ~190 nucleotides in length [38], far too long a sequence to have arisen through any conceivable process of random assembly. And typically 10,000,000,000,000-1,000,000,000,000,000 randomized RNA molecules are required as a starting point for the isolation of ribozymic and/or binding activity in in vitro selection experiments, completely divorced from the probable prebiotic situation. As Charles Carter, in a published review of our recent paper in Biology Direct[5], puts it:

“I, for one, have never subscribed to this view of the origin of life, and I am by no means alone. The RNA world hypothesis is driven almost entirely by the flow of data from very high technology combinatorial libraries, whose relationship to the prebiotic world is anything but worthy of “unanimous support”. There are several serious problems associated with it, and I view it as little more than a popular fantasy” (reviewer's report in [5]).

1014-1016is an awful lot of RNA molecules. However, the discovery of a number of extremely short ribozymes suggests that long sequences – and hence the huge numbers of RNA molecules required to sample the necessary sequence space – might not have been necessary. In a section titled ‘Miniribozymes: small is beautiful, Landweber and colleagues [31] discuss a number of such small ribozymes, including a minimal size active duplex of only 7 nucleotides that self-cleaves. Regarding the relatively modest rate enhancement of this miniribozyme – three orders of magnitude less than the parent ribozyme from which it is derived – the authors conclude: “the smallest molecules are likely to arise first, and any rate enhancement would have been beneficial in a prebiotic setting” [31]. Another, closely related, miniribozyme can ligate a small RNA to its 5′ end, requiring only a single(!) bulged nucleotide in the context of a larger base-paired structure containing a strand break. Interestingly, the self-cleaving 7-nucleotide sequence forms a part of the ligase ribozyme, demonstrating the closeness in sequence space of the two, albeit related, functions [31]. Equally as interesting from an RNA world perspective, Yarus and colleagues have recently isolated by in vitro selection a ribozyme that is able to be truncated to just 5 nucleotides, while retaining its ability to catalyze the aminoacylation in trans of a 4-nucleotide RNA substrate [39]. Remarkably, only 3 nucleotides are responsible for this activity: 2 in the ribozyme and 1 in the substrate. In fact, even this much is not required: a variant of the parent ribozyme with a mutation of 1 of the 3 conserved nucleotides is able to aminoacylate a substrate variant with the sequence GCCA (similar to the universal aminoacylated 3′ terminus of tRNA), albeit at a reduced rate [40] (we have previously proposed a possible sequence for an aminoacylating ribozyme based on this variant that could have base-paired with the universal 3′ CCA termini of tRNAs (and proposed RNA hairpin precursors [41, 3] through a double helix interaction, while also forming specific triple helix interactions – at acidic pH – with other nucleotides in the tRNA [5]). As with the small ribozymes discussed by Landweber and colleagues, the rates of aminoacylation of Yarus' ribozymes are somewhat underwhelming: that of the original 5-nucleotide ribozyme is only 25-fold higher than the uncatalyzed rate [39], while that of the variant is only 6-fold higher than the uncatalyzed rate [40] (for further discussion of the implications of such tiny ribozymes see [42], and [31] and references therein).

Although not quite as small as the ribozymes discussed above, Gross and colleagues have demonstrated that 12-nucleotide and 20-nucleotide nuclear tRNATyr introns from Arabidopsis thaliana and Homo sapiens – understood to be cleaved by protein enzymes in vivo – are able to self-cleave in the presence of 10 mM Mg2+, 0.5 mM spermine and 0.4% Triton X-100 [4345]. Although the introns form part of a larger pre-tRNA sequence, the nucleotides responsible for self-excision are possibly confined to a 3- or 4-nucleotide bulge region. The discovery of this intrinsic activity (which admittedly requires the presence of a low concentration of surfactant) supports previous proposals for the origin of tRNA [41, 3, 4]. Although there exist a number of other models for the origin of tRNA (one of which is discussed in detail in the following section), a hairpin duplication-ligation origin stands as a credible hypothesis [41, 3] that has received support from a number of sources [4648]. Briefly, the idea - first proposed by Di Giulio [41] - is that two (either identical or very similar) hairpins, approximately half the size of contemporary tRNA, formed a ligated duplex due to the symmetry of base-pairing interactions, possibly by an intron-mediated mechanism [49] (Figure1). It has been proposed previously that contemporary protein-spliced nuclear tRNA introns are descended from an ancestral self-splicing group I-type intron that catalyzed the ancestral ligation [49] (as depicted in Figure1, the ancestral tRNA intron may have derived from a 3′ extension of one of the precursor hairpins by a transcriptional runoff error). The findings of Gross and colleagues [4345] indicate that some normally protein-cleaved nuclear tRNA introns have partially retained the ability to self-cleave. This ability to self-cleave implies the reverse reaction – self-ligation – is also possible, which could have produced the ligated intron-containing hairpin intermediate; subsequent intron self-cleavage could have produced the first proto-tRNA [49] (Figure1).
Figure 1

A proposal for the origin of tRNA through the ligation of a hairpin duplex catalyzed by an ancestral self-splicing group I-type intron based on proposals by Di Giulio [41], and Dick and Schamel [49]. In this depiction, the intron is shown as originating from a 3′ extension of one of the precursor hairpins formed by a transcriptional runoff error. aa indicates the amino acid binding site, but is not meant to imply that an amino acid was necessarily attached here during the intron ligation events.

The catalytic repertoire of RNA is too limited

It has been suggested that the probable metabolic requirements of an RNA world [50] would have exceeded the catalytic capacity of RNA. The majority of naturally occurring ribozymes catalyze phosphoryl transfer reactions – the making and breaking of RNA phosphodiester bonds [51]. Although the most efficient of these ribozymes catalyze the reaction at a comparable rate to protein enzymes – and in vitro selection has isolated ribozymes with a far wider range of catalytic abilities [9, 51] – the estimate of proteins being one million times fitter than RNA as catalysts seems reasonable, presumably due to proteins being composed of 22 chemically rather different amino acids as opposed to the 4 very similar nucleotides of RNA [12].

It is frequently forgotten however that proteins too have their catalytic limitations: after all, many enzyme active sites contain cofactors and/or coordinated metal ions, suggesting that some reactions are ‘too hard’ for proteins as well (it is estimated that ~50% of proteins are metalloproteins [52], although of course not all these metal ions are found at the active site). RNA riboswitches bind a range of protein cofactors, such as flavin mononucleotide, thiamine pyrophosphate, tetrahydrofolate, S-adenosylmethionine and adenosylcobalamin (a form of vitamin B12) [53]. In the case of the glmS riboswitch/ribozyme, the metabolite glucosamine-6-phosphate binds in the active site and appears to participate in catalysis [54]. Because of the ability of these naturally occurring RNA riboswitches to bind protein enzyme cofactors, and because many of these cofactors possess non-functional fragments of RNA – one of the earliest pointers to a possible ancestral RNA world [55] – it is likely that at least some of the cofactors now used by proteins were handed down directly from the RNA world, where they played a similar if not identical role in assisting catalytic function [53].

One of the arguments for the RNA world hypothesis comes from the observation that RNAs are, in most cases, worse catalysts than proteins. This implies that their presence in modern biological systems can best be explained by their being remnants of an earlier stage of evolution, which were too embedded in biological systems to allow replacement easily. An alternative explanation is that they were co-opted by a protein world due to their superior properties for the particular functions they perform. While such an explanation seems intuitively less likely, surprisingly it is held by some proponents of the ‘proteins first’ model [5660] (discussed in more detail below).

Proteins first

An increasingly strident view is that protein either preceded RNA in evolution or, at the very least, that RNA and protein coevolved, in what is known as the ‘proteins (or peptides) first’ hypothesis [5660]. Take, for example, Charles Kurland in his 2010 piece in Bioessays[57], which is utterly scathing of the RNA world hypothesis and its fellow travelers:

“[The RNA world hypothesis] has been reduced by ritual abuse to something like a creationist mantra”, and

“[The] RNA world is an expression of the infatuation of molecular biologists with base pairing in nucleic acids played out in a one-dimensional space with no reference to time or energy” [57].

On a less emotional note, Harish and Caetano-Anollés [60] earlier this year published a phylogenetic analysis of ribosomal RNA and ribosomal proteins, concluding that the oldest region of the ribosome is a helical stem of the small ribosomal subunit RNA and the ribosomal protein that binds to it. As this helical stem has the important roles in the modern ribosome of decoding the mRNA message and in the movement of the two subunits relative to each other (including translocation of the mRNA message and tRNAs), Harish and Caetano-Anollés conclude that the original function of the ribosome was as an RNA replicase (this idea, which has been suggested previously, is discussed in detail in the following section). In addition, because RNA and protein components of the ribosome apparently have similar ages, Harish and Caetano-Anollés surmise that peptide synthesis has always been carried out by RNA in association with proteins, as is the case with the modern ribosome.

Without debating the merits or otherwise of their phylogenetic techniques, the most serious objection to these conclusions is that phylogenetic analysis has the limitation that it can only analyze the protein sequence record as it has been captured in DNA (this is true even for a phylogenetic analysis based on protein fold structures, as the only record we possess of these folds is their primary amino acid sequence as captured in the DNA). Therefore, any information we can recover can only date from the advent of coded protein synthesis, as that is the point at which protein sequence became coded in nucleic acid. In an online report [61] on Harish and Caetano-Anollés’ paper, Russell Doolittle makes this same point:

“This is a very engaging and provocative article by one of the most innovative and productive researchers in the field of protein evolution,” said University of California at San Diego research professor Russell Doolittle, who was not involved in the study. Doolittle remains puzzled, however, by “the notion that some early proteins were made before the evolution of the ribosome as a protein-manufacturing system.” He wondered how – if proteins were more ancient than the ribosomal machinery that today produces most of them –“the amino acid sequences of those early proteins were ‘remembered’ and incorporated into the new system.” [61].

To which, Caetano-Anollés’ reported response is slightly puzzling:

“It requires understanding the boundaries of emergent biological functions during the very early stages of protein evolution. However, the proteins that catalyze non-ribosomal protein synthesis – a complex and apparently universal assembly-line process of the cell that does not involve RNA molecules and can still retain high levels of specificity – are more ancient than ribosomal proteins. It is therefore likely that the ribosomes were not the first biological machines to synthesize proteins.” ([61]; italics in original).

It is certainly possible that there were functional noncoded peptides prior to the advent of coded protein synthesis. These could have been formed either through random processes, by noncoded ribosomal synthesis prior to the advent of coding [4], by non-ribosomal peptide synthesis catalyzed by specific ribozymes (analogous to non-ribosomal peptide synthesis catalyzed by protein enzymes in modern systems [62]), or by some combination of the above. It seems highly unlikely, however, that proteins synthesized proteins prior to the advent of the ribosome, as this would appear to suggest an infinite regression series. As Doolittle [61] suggests, the critical point is that once coding evolved, the sequences of these noncoded proteins would have needed to be recapitulated by coded proteins; therefore the phylogenetic signal would only go back to the point of recapitulation. Put another way, the earliest proteins phylogenetically speaking will be the first proteins that were coded for. Presumably, if these sequences can still be detected in modern genomes, they would tend to be relatively short and somewhat indistinct traces only, as one might expect for the first proteins produced by a rudimentary ribosome. In a sense then, one can say that the advent of coded protein synthesis has drawn a veil over the previous life of proteins. Although it seems unlikely, complex proteins may have existed prior to this, but – as all record of them has been erased by the advent of coding – that is as much as we can say (for an in-depth discussion of the implications of non-ribosomal peptide synthesis for the RNA world hypothesis, see [62]).

RNA replicase origin of the ribosome

As mentioned above, Harish and Caetano-Anollés are not the first to suggest an RNA replicase origin of the ribosome (or small ribosomal subunit). The idea, which was possibly first proposed by Weiss and Cherry [63], is that “the ancestor of small subunit RNA was an RNA replicase that used oligonucleotides as a substrate” [63]. The hypothesis has grown in scope to include the use of excised tRNA anticodons as the source of oligonucleotides, with the energy required for ligation provided by concomitant peptide bond formation [6466]. However, as pointed out by Wolf and Koonin [67], such a ligase would have required a molecular machinery at least as complex as the modern ribosome, which would make it an unlikely evolutionary forerunner. This notwithstanding, Weiss and Cherry’s original, simpler, model may have some merit. If, as has been recently suggested, early RNA replication was performed by the ligation of short oligonucleotides [68, 69], or by a combination of nucleotide polymerization and oligonucleotide ligation [21], a ‘decoding’ RNA able to proofread triplet base pair interactions for accuracy – similar to its role in the modern ribosome of maintaining the fidelity of the triplet codon-anticodon interaction – might have played an important role. Interestingly, a 49-nucleotide hairpin comprising part of the decoding site of the small ribosomal subunit RNA has been found to bind both poly U oligonucleotide and the tRNAPhe anticodon stem-loop in a similar fashion to the entire small subunit [70]. This hairpin contains the two mobile nucleotides A1492 and A1493 (numbered according to the Escherichia coli small ribosomal subunit RNA sequence) that proofread the anticodon-codon helix in the modern ribosome [71]. It would be interesting to test whether this hairpin is able to enhance the rate and/or accuracy of non-enzymatic ligation using a single-stranded RNA ‘template’ and short complementary oligonucleotides. If an enhancement were indeed demonstrated, such a mechanism would be analogous to that utilized by the large ribosomal subunit, for which substrate positioning of the two tRNAs may constitute one of its main roles in catalyzing peptide synthesis [72].

As part of their model of early RNA replication by oligonucleotide ligation, Manrubia and colleagues propose that an increase in the catalytic rate of the replicase/ligase would have occurred with an increase in sequence length through a process of bootstrapping [68, 69]. Furthermore, they suggest that the first RNA replication possibly had a high error-rate:

“Highly mutagenic replication processes could have produced relatively large repertoires of short, genetically different molecules, some of them folding into secondary/tertiary structures able to perform selectable functions” [68].

Similarly, we have proposed that, in an RNA world evolving at acidic pH, non-standard base pairing interactions due to base protonation could have provided a means of increasing RNA sequence variation through non-enzymatic replication [5].

The origin of tRNA

Wiener and Maizels’ genomic tag hypothesis proposes that the 3′ (or ‘top’) half of tRNA originally functioned as a tag demarking the 3′-end of genomic RNAs for replication, and thus was the first part of tRNA to evolve [73]. Sun and Caetano-Anollés [74, 75] have published phylogenetic evidence that they believe supports the genomic tag hypothesis by confirming, “that the ‘top half’ of tRNA is more ancient than the ‘bottom half’” [75]. Noller [76] has observed that the tRNA top half (comprising the T arm and the acceptor stem – including the amino acid binding site) interacts almost exclusively with the large ribosomal subunit, while the bottom half (comprising the D and anticodon arms) interacts almost exclusively with the small subunit. Because peptide synthesis (a function of the large subunit) is usually viewed as more ancestral than decoding (a function of the small subunit) – a view which has support from a structural analysis by Bokov and Steinberg [77] – the top half of tRNA (which interacts with the large subunit) has been viewed as being more ancestral than the bottom half [73, 78]. However, this ‘standard model’ for the origin of tRNA, and the results of Sun and Caetano-Anollés that support this model [74, 75], are apparently both in conflict with Harish and Caetano-Anollés’ [60] more recent findings on the relative ages of the ribosomal subunits. As described above, these findings suggest that the small ribosomal subunit was the first to evolve, which is difficult to reconcile with the fact that the bottom half of tRNA (with which the small subunit mainly interacts), is, by theirs [74, 75] and others [73, 78] estimation, the newer half of tRNA. Equally, their finding that the large ribosomal subunit evolved more recently [60] is difficult to reconcile with the fact that the top half of tRNA (with which the large subunit mainly interacts), is, by theirs and others estimation, the older half of tRNA. Incidentally, Caetano-Anollés and colleagues’ finding [75, 79, 80] that the most ancient tRNAs coded for selenocysteine, tyrosine, serine and leucine not only runs counter to other work in the area (see e.g.[81]), but – as these tRNAs all possess long variable arms – appears to contradict their own finding that the “variable region was the last structural addition to the molecular repertoire of evolving tRNA substructures” [74].

As discussed above, a plausible scenario for the origin of tRNA is the duplication and subsequent ligation of an RNA hairpin approximately half the length of modern tRNA (or alternatively the ligation of two very similar hairpins) [41, 3], with ligation possibly catalyzed by an ancestral self-cleaving intron [49] (see Figure1). An important implication of such an origin is that both tRNA halves are of equal antiquity, as both would have to be present for ligation to occur! However, due to the symmetry of the tRNA molecule, the top half, which is considered to be the more ancient, is in fact more ancient-like, as it retains the base-paired 3′ and 5′ ends of the original hairpin from which it derives. In contrast, the bottom half, considered to be the more recently acquired, contains the ‘join’ between the two hairpins, which has altered the conformation of the original hairpin, giving this bottom half a new structure. If one accepts a hairpin duplication-ligation origin of tRNA, this explains why the top half of tRNA interacts with the peptidyl transferase region of the large ribosomal subunit: it is because this half retains the same structure (and possibly nucleotide sequence) as the hairpin from which it derives, which originally interacted with the peptidyl transferase region of the large subunit. In fact - and this point has been made by others [49] – this retention of structure probably favoured (or even enabled) the duplication event, as it meant the resultant tRNA was able to be aminoacylated by the same ribozyme synthetase that aminoacylated the hairpin precursor, and therefore the tRNA was able to participate in ribosomal protein synthesis. At the same time, the appearance of a novel structure at the ligation point – the anticodon loop – allowed for the subsequent evolution of genetic coding [4, 3].

One of the strongest arguments in favour of the hairpin ligation being catalyzed by an ancestral self-cleaving intron [49] (as depicted in Figure1) is the presence of the highly conserved ‘canonical intron insertion position’ between nucleotides 37 and 38 in the anticodon loop [41], where almost all eukaryotic nuclear (and the majority of archaeal) tRNA introns are found, even though introns are only found in a subset of tRNA isoacceptors [82]. It has been proposed previously that this conserved position constitutes a 'molecular memory’ of the position of the ancestral intron that was responsible for the ligation that created the first tRNA [83]. If the canonical intron insertion position is ancestral, it implies that eukaryotic nuclear tRNAs (and possibly archaeal tRNAs) have a more ancestral structure than eubacterial tRNAs, which usually lack tRNA introns altogether or possess self-splicing introns at a variety of different positions in the molecule. Such a finding is consistent with the introns-early hypothesis, and the proposal that eubacteria have undergone a process of intron loss [84, 85].

I have argued that the RNA world hypothesis, while certainly imperfect, is the best model we currently have for the early evolution of life. While the hypothesis does not exclude a number of possibilities for what – if anything – preceded RNA, unfortunately the evolution of coded protein synthesis has drawn a veil over the previous history of proteins. The situation is different in the case of non-coding RNAs such as ribosomal RNA and tRNA, as these were able to replicate prior to the evolution of ribosomal protein synthesis.

As we have noted previously [5], the proposal that the RNA world evolved in acidic conditions [5, 6] offers a plausible solution to Charles Kurland's criticism [57] that the RNA world hypothesis makes no reference to a possible energy source. As de Duve [87] has noted, "the widespread use of proton-motive force for energy transduction throughout the living world today is explained as a legacy of a highly acidic prebiotic environment and may be viewed as a clue to the existence of such an environment" [87]. Although Russell, Martin and others [2326] have argued that proton and thermal gradients between the outflow from hot alkaline (pH 9-11) under-sea hydrothermal vents and the surrounding cooler more acidic ocean may have constituted the first sources of energy at the origin of life, the lack of RNA stability at alkaline pH ([5] and references within) would appear to make such vents an unlikely location for RNA world evolution.

Although possible, it seems unlikely that the A-C base pair 'mismatches' found in the tRNA genes of Ferroplasma acidarmanus and Picrophilus torridus (two species of archaebacteria with a reportedly acidic internal pH) [5] are corrected by C to U RNA editing that occurs, for example, with some - but not other - plant chloroplast tRNAs [88, 89]. Such editing of secondary structure A-C base pair mismatches has so far not been found to occur in archaebacteria; however, in a single archaeal species (Methanopyrus kandleri) a tertiary structure A-C base pair found in 30 of its 34 tRNAs undergoes C to U editing catalyzed by a cytidine deaminase CDAT8 [90]. M. kandleri is a unique organism that contains many 'orphan' proteins. CDAT8, which contains a cytidine deaminase domain and putative RNA-binding domain, has no homologues in other arachaeal species, including F. acidarmanus and P. torridus (L Randau, pers. commun.; [90]). Definitive proof, however, that the A-C base pairs in these two species are not modified would of course require e.g. cDNA sequencing of the tRNAs.

Reviewers’ comments

Referee 1: Eugene Koonin

I basically agree with Bernhardt. The RNA World scenario is bad as a scientific hypothesis: it is hardly falsifiable and is extremely difficult to verify due to a great number of holes in the most important parts. To wit, no one has achieved bona fide self-replication of RNA which is the cornerstone of the RNA World. Nevertheless, there is a lot going for the RNA World (Bernhardt summarizes much of the evidence, and I add more below) whereas the other hypotheses on the origin of life are outright helpless. Moreover, as argued in some detail elsewhere [91], the RNA World appears to be an outright logical inevitability. ‘Something’ had to start efficiently replicating to kick off evolution, and proteins do not have this ability. As Bernhardt rightly points out, it is not certain that RNA was the first replicator but it does seem certain that it was the first ‘good’ replicator. To clarify, this does not imply that the primordial RNA World did not have peptides; on the contrary, it is plausible that peptides played important roles but they were not initially encoded in RNA.

Moreover, straightforward observations on modern proteins indicate that the role of RNA in the ancient translation system was much greater that it is in the modern system. Indeed, Class I aminoacyl-tRNA synthetases (aaRS) represent only a small branch on the complex evolutionary tree of Rossmann-like domains, so the common ancestor of all 10 Class I aaRS emerged after extensive diversification of this particular class of protein domains had already taken place. Accordingly, one is compelled to conclude that a high-fidelity translation system that alone would enable extensive protein evolution existed already at the late stages of the hypothetical RNA World [92].

All this discussion is not pointless play with hypotheses. Realization of the unique status of the RNA World among the origin of life scenarios is critical for maintaining the focus of research on truly important directions such as experimental and theoretical study of the evolution of ribozymes rather than futile attempts to debunk the RNA World.

Referee 2: Anthony Poole

Harold Bernhardt’s review of the RNA world hypothesis is readable and timely. He presents a very open-minded review of recent results and how they impact on old ideas, and distills a large amount of material. Aside from the admirable attempt to synthesize a vast array of ideas, a valuable contribution hidden within is the critical assessment of the view that the RNA world hypothesis needs to be abandoned in favour of a peptides-first model.

Author’s response: I have revised the abstract and introduction to include reference to my critique of the ‘proteins (or peptides) first’ hypothesis.

While I doubt that anyone seriously excluded peptides as part of a prebiotic milieu, the primacy of peptides does need careful consideration. In this regard, the explicit explanation of why a pre-genetic code origin of proteins will not be detectable from comparative genomic analyses is an important contribution. Perhaps this is obvious to some, but in light of a growing view that non-ribosomal peptide synthesis preceded ribosomal peptide synthesis, it would seem that the community needs a reminder, and Bernhardt spells it out in a very informative manner. Another issue with arguing for non-ribosomal peptide synthesis preceding the ribosome is that there is an enormous difference in information input versus output. As discussed in [[62]], megaenzymes like cyclosporin are ~15000 amino acids in length and produce products of 11 amino acids in length – a factor of 10 4 is not trivial. While non-ribosomal peptide synthetases are modular and could in principle be engineered into minimal entities, the challenge of equalizing information input and output is significant regardless of one’s favoured prebiotic starting point. It is clear from reading Bernhardt’s review that the RNA community is much closer to this than those who seek to replace primordial RNA-based replication with peptide-based replication.

Referee 3: Michael Yarus (nominated by Laura Landweber)

Almost always, progress to new understanding is sporadic, with insights coming in separated locales. Difficulties temporarily immobilize discussion, but then are surmounted by a successful theory. This sometimes inchoate stagger toward a broader, more self-consistent argument is all that can be expected, even of an ultimately successful idea. Discussions of the RNA world sometimes forget this, and demand e.g., the ultimate replicase today! But this essay by Harold Bernhardt remembers what has happened for other successful evolutionary ideas, like the big tree. For all its successes, the tree is still being questioned under extreme prejudice in certain quarters, as is the RNA world.

Contrariwise, here we have here a sympathetic review of the support for the RNA world, which specifically makes the point that it fits our descent better than other ideas (You look like the son of a montmorillonite to me, ya mangy mutant!). It will be useful to those who want an entry to the RNA world literature, and could easily serve as the crux of a university course.

However, this is also its weakness; the text is polite and respectful, even to those whose ‘contribution’ has been otherwise. It treats even loony ideas (‘we need proteins to evolve translation!’) with deference. Or to put it in other words, it is edgeless – some attitude would be welcome. Some choice between hypotheses should go with the territory; some consequent make-or-break predictions are the responsibilities of a guide. But as a gentle introduction, you will not find better.

Author’s response: In revising the manuscript, I have – to some degree inadvertently – added a bit more bite!

messenger RNA

transfer RNA.

This paper is dedicated to my mentor and colleague Professor Warren Tate, who was instrumental in my setting off on this life of adventure and discovery and who encouraged me to write this paper. Many thanks to Hans Gross, George Fox and Steven Benner for critical reading of an early draft of this manuscript and for their helpful suggestions. Thanks to Lennart Randau for helpful information regarding his work on CDAT8 from M. kandleri. Thanks to Diana Yates from the University of Illinois News Service and Russell Doolittle for permission to use material which first appeared there. The research was conducted during tenure of a Health Sciences Career Development Award at the University of Otago.

The title is an adaptation of Sir Winston Churchill’s famous comment on democracy made in a speech to the House of Commons on 11 November 1947: No one pretends that democracy is perfect or all-wise. Indeed, it has been said that democracy is the worst form of government except all those other forms that have been tried from time to time.

Authors’ Affiliations

Department of Biochemistry, University of Otago

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All the work is designed and handmade by Ruchi Gupta in her ceramic studio at Richmond, Virginia.

Paulus Berensohn - Finding one's way with clay is a technical question: in what way, i.e method do I want to work? It is also a question of style: How do I want the piece to look? And it is a spiritual question as well: How do I relate?......

Birds at noon is Ruchi's studio where ideas get tangible form through clay.

My Story I was born and raised in India, in a small town called Ajmer, in Rajasthan. My dream was to live in an invisible house, read books and draw for a living.... but reality took it's toll and I ended up climbing winding staircase of corporate world.

After wandering around the grey corridors for a decade, a little bird inside me led me back to my childhood dream. I got introduced to this amazing world of creating and making where you can give shape to your ideas. I call it Birds at Noon....

Today, I am a full time ceramic artist, working in clay, drawing, painting, reading and learning to open windows of my invisible house.

My Work I am on a journey of exploration, expression and creation; trying to find my way through clay. I do not strive for perfection, but be led by the flow, which I get being in that moment.

Mythology, symbols, text, antiques, cultures and history intrigue me. I am drawn to the richness of color, texture and architecture.

My designs are the borrowings from my upbringing in India, the swatch of colors that fill my memory. The drawings are the objects and places that aroused my curiosity. Every layer tells a story, which I experienced in making and living.

Ruchi Gupta

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Katherine Todd

Marketing n Studio

Sumeet Gupta

Samyak Gupta

To be open to the needs of growth: to ripen as clay ripens, through geology and the weathering of the storms. Ira ProGoff says ~ It is not a trip but a whole journey....

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An estimated 30 percent of US women will have an abortion in their lifetimes. Globally, 13 percent of all pregnancies in Africa, 40 percent in Latin America and 29 percent in Asia end in abortion—a total of 36 million annually. Despite the continued need for safe and accessible abortion care, research opportunities are limited and there is a shortage of trained providers worldwide.

The Bixby Center is one of the few research institutions to unflinchingly address abortion, investigating multidimensional aspects of abortion care in the United States and globally. Our work has:

Clinical care

The Bixby Center has been a leader in clinical research to develop methods of abortion and improve abortion care. Our research demonstrated the efficacy, safety and acceptability of the combined use of mifepristone and misoprostol for early abortion. We have continued to lead clinical trials to improve abortion safety and access. And our researchers are examining the kinds of abortion care women prefer in specific contexts.

Social science research

Our program Advancing New Standards in Reproductive Health (ANSIRH) leads innovative, rigorous studies of abortion. For example, ANSIRH’s Turnaway Study examines the mental, emotional, physical and socioeconomic consequences of abortion. It involves almost 1,000 women who sought abortions at 30 clinics around the United States. Some of the women received abortions while others were denied the procedure because of clinic or state policies. Additional ANSIRH research is focused on integrating abortion into primary care, the effects of state abortion restrictions, provider experiences, and cultural narratives about abortion in film and television.

One of the few recent state laws expanding access to abortion care was grounded in Bixby research. California affirmed that nurse practitioners, certified nurse midwives and physician assistants can safely perform early abortions.

Training providers

Our extensive training programs are helping address the lack of abortion training and integration of family planning into medical education. Before 1999, less than 15 percent of obstetrics and gynecology residency training programs provided routine abortion training. Though our Ryan Residency Training Program, which provides ob-gyn residents  the opportunity to develop clinical and research skills in abortion and contraception, we've doubled the number of programs addressing these critical women's health issues. Additionally, the Fellowship in Family Planning trains subspecialty leaders in family planning and research methods. Graduated fellows have become experts and leaders in academic medical centers, teaching hospitals, NGOs and research institutions globally.


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Blackhawks beat Hurricanes in shootout

Kurt Dusterberg  - Correspondent | Tuesday, 10.15.2013 / 11:33 PM

RALEIGH, N.C. -- In a sport full of athletes who are quick to deflect too much praise or credit, Chicago forward Patrick Sharp couldn't escape being the focus after the Blackhawks' 3-2 shootout win over the Carolina Hurricanes.

Sure, he scored the first goal of the game, chasing down an aerial pass at the Carolina blue line before scoring his second of the season at 7:56 of the opening period. Then he scored the only goal of the shootout to secure a 3-2 win and lift Chicago to a 4-1-1 record. That's more than enough reason to be the media's go-to guy after the game.

But the goals were just the start.

Sharp's big night came just two days after the birth of his second daughter, making Tuesday night's game one of those occasions where life and hockey intersect at a place that transcends a particular game.

"My head wasn't really in the game for the first part of it," Sharp admitted. "But it's a special time for the family and I'm looking forward to getting home."

That's because Sharp felt a little paternal concern after leaving his growing family behind in Chicago.

"I felt a little guilty leaving Sunday and going to practice on Monday with my wife in the hospital," he said. "She was in great hands. Her mother is here taking care of our first daughter and our dog and the house."

With things in reasonable order back home, Sharp was free to contribute in a game the Blackhawks needed him.

After Michal Handzus fed him a perfect home-run pass for the first goal -- the 200th of Sharp's career -- Marian Hossa made it 2-0 at 10:18 when Carolina defenseman Brett Bellemore whiffed on a clearing pass in the slot. Hossa lifted a backhand past Cam Ward, who was moving right to left on the play.

At that point, it looked like Chicago might run away with the game. The Blackhawks outshot the Hurricanes 15-5 in the first period and controlled play for long stretches.

Chicago led 2-0 after two periods before the Hurricanes broke through in the third. Alexander Semin cut the lead in half at 3:54 when he gathered the rebound of Eric Staal's shot and beat goaltender Corey Crawford over the glove. With 7:27 remaining in regulation, Ron Hainsey's low blast from the left point found its way inside the far post to tie the game at 2-2.

"You have to give them credit," Hossa said. "They came back and showed they're a really good hockey team with lots of skilled players. We let off the gas a little bit and they scored and all of a sudden the game was tied."

Heading to overtime insured the Blackhawks a fifth straight one-goal game.

"That third goal, we were all looking to get that," Chicago coach Joel Quenneville said. "It might have made things a little bit more comfortable."

Instead, things grew more unsettling as the teams went to overtime. The Blackhawks had to kill a 4-on-3 Carolina power play in which the Hurricanes tested Crawford with four shots. At one point, defenseman Brent Seabrook lost his stick, leaving the Blackhawks in a pinch until Crawford was able to freeze the puck.

Then came the shootout, in which Crawford gave Nathan Gerbe, Alex Semin and Jeff Skinner no daylight. Sharp, the third shooter for Chicago, came in deliberately against Ward before deking and sliding the puck inside the left post.

"Some nights you are not happy with the execution, but we had no time out late to give them a rest," Hurricanes coach Kirk Muller said. "The chances were there, we tried it, and Crawford came up with some big saves. It was just a really entertaining, hard-fought game that these two teams played."

For Sharp, the shootout goal was a nice bonus, since he doesn't think of himself a strong alternative in the tiebreaker.

"I haven't been very good in the shootout the last couple years," Sharp said. "I looked at that over the summer and thought about some possible moves with [Patrick] Kane a little bit. [Skating in slowly] was actually by design. I don't have hands like Kaner, so the slower I go, the better mine get."

On a night when Sharp was the difference in the game, he was glad to share a few personal moments.

How does it feel to score 200 NHL goals?

"It's something I'll look at when I'm all said and done," he said. "Hopefully I've got a lot more than 200. I'd like to play a lot more years and score a lot more goals."

And what about the puck from No. 200th?

"I'll send it back home to my parents in Thunder Bay [Ontario]. They have all my milestone pucks."

Then Sharp volunteered that he's already planned another keepsake.

"I kept the shootout puck," he said. "That's for my daughter, and the stick will be with her as well. Start spoiling her early."

Scoring Summary
1st Period
07:56CHI Patrick Sharp (1) ASST: Michal Handzus (2) 1 - 0 CHI
10:18CHI Marian Hossa (2) ASST: Brandon Saad (3), Andrew Shaw (2) 2 - 0 CHI
2nd Period
3rd Period
03:54CAR Alexander Semin (2) ASST: Eric Staal (2), Tuomo Ruutu (1) 2 - 1 CHI
12:33CAR Ron Hainsey (1) ASST: NONE 2 - 2 Tie
OT Period
1CHIPatrick Kane - Save
2CARNathan Gerbe - Save
3CHIJonathan Toews - Save
4CARAlexander Semin - Missed
5CHIPatrick Sharp - Goal
6CARJeff Skinner - Save
Shootout Summary
RNDChicago BlackhawksCarolina Hurricanes
1Patrick KaneNathan Gerbe
2Jonathan ToewsAlexander Semin
3Patrick SharpJeff Skinner
Three Stars of the Game
Corey Crawford
Corey Crawford
SA: 34TOI: 64:41
GA: 2EV: 29-31
PIM: 0PP: 3-3
SV%: .941SH: 0-0
Cam Ward
Cam Ward
SA: 36TOI: 64:51
GA: 2EV: 32-34
PIM: 0PP: 2-2
SV%: .944SH: 0-0
Marian Hossa
Marian Hossa
G: 1Shots: 4
A: 0Hits: 0
PTS: 1PIM: 0
+/-: 2TOI: 16:20
Penalty Summary
1st Period
08:15CAR Eric Staal  Holding against  Johnny Oduya
2nd Period
02:48CHI Michal Rozsival  Interference against  Brett Sutter
03:47CAR Drayson Bowman  Too many men/ice - bench
09:05CHI Johnny Oduya  Hooking against  Patrick Dwyer
3rd Period
04:31CAR Ron Hainsey  Holding against  Andrew Shaw
15:33CHI Michal Rozsival  Slashing against  Jeff Skinner
OT Period
02:30CHI Bryan Bickell  Hooking against  Ryan Murphy
shots by period
Team Stats
Power Plays0/30/4
Faceoff Wins2944
Blocked Shots2613
Penalty Minutes86
2D. KeithD0004025:14
4N. HjalmarssonD0000026:00
7B. SeabrookD0013023:31
8N. LeddyD0001013:25
10P. SharpL1004016:32
16M. KrugerC0000015:20
19J. ToewsC0002021:38
20B. SaadL0104016:40
26M. HandzusC0101014:34
27J. OduyaD0000226:05
28B. SmithR0001010:38
29B. BickellL0001217:31
32M. RozsivalD00-10413:27
42J. NordstromL00-22010:29
52B. BolligL000009:14
65A. ShawC0104015:23
81M. HossaR1024016:20
88P. KaneR0005020:18
50C. Crawford3234.94164:41
4A. SekeraD0003023:51
7R. MurphyD0013025:01
11J. StaalC0001020:31
12E. StaalC01-14223:11
14N. GerbeC00-12018:50
15T. RuutuL0103017:13
18R. DvorakR001209:36
19J. TlustyL0001012:47
20R. NashC0000015:42
21D. BowmanL0001010:23
27J. FaulkD0011024:34
28A. SeminR1006023:00
39P. DwyerR0002013:27
42B. SutterL000005:42
44J. HarrisonD0010021:18
53J. SkinnerL0014019:07
65R. HainseyD10-11218:11
73B. BellemoreD00-20011:46
30C. Ward3436.94464:51


WARC-Truncated: length

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Torii Hunter, Darius McClinton-Hunter

Darius McClinton-Hunter, left, and his father Torii Hunter, baseball player with the Los Angeles Angels, attend a news conference Thursday, May 17, 2012, in Plano, Texas. Todd Shapiro the attorney defending 17-year-old McClinton-Hunter told reporters that a recording was made Wednesday of a conversation between the 16-year-old alleged victim and a teenage friend of the Hunter family recanting sexual assault accusation. Prosper, Texas police arrested McClinton-Hunter Monday for sexual assault. (AP Photo/The Dallas Morning News, Lara Solt)


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Dec 29, 2007

Your Friend the Rat-the Little Golden Book version

If you haven't been by Jim Capobiano's blog lately you might not yet know that there's a new Little Golden Book out that's going to be a must-have. It's a companion piece to his wonderful short film "Your Friend The Rat" that debuted on the "Ratatouille" DVD release.

I snagged the above image from the Amazon website, which is where I suspect Jim got the cover shot he posts on his blog; he says the color is off and he'll soon post a more accurate one(it's really got to annoy when one works so hard on these things to see wrong color advertising it anywhere). For more information about it, hie yourselves over to Jim's blog pronto.
He's been busy putting up some very interesting posts with behind the scenes tidbits about the making of his film-this is really gold.
photo of Scott Morse by Jim Capobianco, courtesy of his blog

I love seeing the process and reading about what people go through at work. Jim had a special added investment, something usually extracurricular to a director/story person's normal plethora of jobs: he cowrote the song that ends the short film. That little song, sung in character by "Remy" and "Emile" was so charming...also pretty darned clever--and the visual accompaniment a tasty treat.

I'm sure the short needs no touting from me to entice anyone to watch it, but honestly, along with the feature itself(a film that I think plays better with repeated viewings-what a pleasure that is to say), it was such a great gift to put it on the DVD. Superior work by everyone, and lots to be inspired by.

gemini82 said...

Thanks for this wonderful post. It is always interesting to see someones process,especially a short film.

I remember watching Alex Woo's Rex Steele Nazi Smasher a few years ago, really interesting behind the scenes material.

Floyd Norman said...

That short film was a real delight. I had the pleasure of working with Jim at both Disney and Pixar.

This talented young man has done good, and I'm looking forward to more cool stuff from him in the future.

samacleod said...

I just saw Dave P's copy, really nice book. Those guys are so productive it makes me sick!

Lee-Roy said...

Oo-oo-ooh! I still haven't watched the DVD and so I have not seen this short! I can't wait! And the book looks great, too!

Exclamation marks!!!


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Padres Pummel Nolasco, Marlins

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Padres Pummel Nolasco, Marlins
Steve Mitchell/Getty Images

MIAMI — The Padres were out to beat the heck out of Ricky Nolasco, the 30-year-old right-hander who's likely in the last of his eight seasons with the Marlins. Mission accomplished. Nolasco was pounded for 11 hits in a 9-2 loss by the National League's worst outfit, a depleted ballclub that's been particularly futile against the Padres, who've shut out the Marlins twice and outscored them 20-3 in four games this season.

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Chad Henne: Week 14 Fantasy Outlook

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Chad Henne: Week 14 Fantasy Outlook

After consecutive 300-yard outings in mid-October, Henne enters Week 14 having tossed for 255 yards or less in five straight games. He'll face a Texans defense which he through for 239 yards against two weeks ago.
Henne has just six touchdown passes all season. While three of those have come in the past three weeks, he didn't score against a stingy Texans defense previously. Further, Houston ranks 2nd in the league in passing yards allowed, rendering Henne to the bottom tier of fantasy quarterbacks.

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LA Clippers Can't Be Judged Until Playoff Time

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LA Clippers Can't Be Judged Until Playoff Time
Getty Images

The Los Angeles Clippers are still trying to make a name for themselves as a legitimate contender after years of being the laughingstock of the National Basketball Association.  The Clippers are trending upwards by enjoying their first year as reigning Pacific Division champions, but playoff success is the true judge.

Come playoff-time, the Clippers haven’t been as productive, as they were bounced by the Memphis Grizzlies last season and the San Antonio Spurs the year before.

This season is no different, as the team sits in its familiar top spot in the Pacific, while being chased again by the Golden State Warriors

Coach Doc Rivers has taken over for Vinny Del Negro, because Doc has a title under his belt and knows how to push and guide a talented squad to the promised land.

If the Clippers want to advance past the exciting team moniker to a legitimate threat, they have a checklist.

The team is growing with the additions of Jared Dudley, J.J. Redick and Darren Collison, a younger group to replace players like Grant Hill and Chauncey Billups.  Collison has been particularly impressive by leading the team to a 6-3 mark through January 22 since the Chris Paul injury.

Effective Ball Movement

As you can see from the highlight, Collison has good court vision and finds DeAndre Jordan for the easy slam.

The free-flow offense and lob city is sustainable in the regular season, but the game slows down in the postseason.  The Clippers must work on the set plays and effective passing around the perimeter.

In this play, the ball is passed around quickly, with Griffin finally setting the screen, rolling off and getting the pass from Redick for the finish.

With their size and quickness, the Clippers have a powerful weapon when used correctly.  If they can consistently toss the ball around the perimeter and move effectively without the ball, the team will have a much better chance of advancing.

This strategy is most prevalent in the post area.  If the team can move the ball effectively during set plays, Griffin and Jordan will have better chances to make athletic plays than have to create on their own.

With Chris Paul at the helm, teams will be keying in on him, which will give the perimeter players like Redick and Matt Barnes more freedom without the ball.  Paul must decide whether to drive the offense or look to distribute to an open weapon.

Paul is the leader in points created by assists per game by a wide margin.  He should be returning soon, as discussed in this tweet.

As great as the offense is on the floor, the defense is the key to moving deep in the playoffs.

Play defense

Playoff games are won in the trenches.  The Clippers need to do a better job on the boards, as they are currently in the middle of the NBA in rebounds and are outrebounded on average by opponents.

Since Jordan leads the league in rebounds and Griffin rips down his share, the rest of the team is not doing its job.

Yes, Jordan has great size and superb athletic skills for a center.  He uses those talents to protect the rim and tally the most blocked shots in the league.

The primary reason for the deficiency is the style of defensive basketball.  The Clips run a stout pick-and-roll defense that requires Griffin and Jordan to trap the ball-handler, in return forcing them further to the perimeter.

The team gave up only 94.6 PPG on average last season, but this year the number has increased to 100.2 PPG.

The system has its vulnerabilities, so Coach Rivers needs to really drill down and fix the holes.  He also needs to improve positioning and one-on-one defending.

The team has improved its defensive efficiency over the past two months, but the team needs to stay consistent if it wants to advance to the Conference finals.

The Bigs on the Bench

Griffin and Jordan are the only two big men with constant production.  If one or both of them get injured or even in foul trouble, the Clips are in danger.

The team is very thin with only Antawn Jamison, Ryan Hollins and Byron Mullens left to take on the responsibility of the lane.

The players hardly get anytime on the floor, as Jamison is the most used with an average of only 11.3 minutes per game.  As a result, Hedo Turkoglu joins the mix.

Turkoglu can fill in at both forward spots, and he can play the small-ball position with a lot of dexterity.  He can draw his man out and hit the jumper or create moves to the hole.

He is not the greatest defender, but he can rely a lot on Dudley and Jordan to fill the gaps.  He is older, but he brings experience and knows how to secure wins.

He doesn’t solve the problem, but he helps solidify one of the biggest weaknesses on this team.  He is a role player who can smoothly transition into wherever the team needs him.

In addition, he has played in the NBA Finals with Orlando and has made countless playoff appearances.

The Bottom Line

The Clippers dominate with a wide-open, fast-moving offense.  The team has all of the pieces in place to make a serious run, but they also face some of the stiffest competition in their own conference.

The Clippers need to fix the holes and further drill down on defense.  Defense wins championships, and a key rebound here and a defensive stop there at crucial moments could really take this group to the next level.

The Clippers want to continue their recent Los Angeles and NBA dominance, and there is no better time than now to solidify their standing.

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NFL Draft 2014: Predicting Where Top Prospects Will Land

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NFL Draft 2014: Predicting Where Top Prospects Will Land
Scott Halleran/Getty Images

NFL draft hopefuls find themselves in a precarious position. They're the most wanted college job applicants in the world, yet they can't determine their future employer.

Unless they pull an Eli Manning, these prospects will sit idly by and hope they get selected by an organization that suits them well. Will they see eye to eye with the coaches? Are the players pleasant colleagues? Do the team's personnel and schemes bode well for playing time and success?

It's a scary day for all members of the 2014 NFL draft class, even those virtually guaranteed a cushy top-10 spot. They still must sweat out the announcement of their future destination in the year's most highly anticipated, jam-packed night of a man reading a name every 10 minutes.

These stars should all be bestowed with a premium first-round selection, but where exactly will they wind up? Let's try to project their new homes after the draft.

NFL Draft - Projecting Top Picks
Team Player School
1. Houston Texans QB Teddy Bridgewater Louisville
2. St. Louis Rams (via Washington) WR Sammy Watkins Clemson
3. Jacksonville Jaguars DE Jadeveon Clowney South Carolina
4. Cleveland Browns QB Johnny Manziel Texas A&M
5. Oakland Raiders QB Blake Bortles Central Florida
6. Atlanta Falcons OLB Khalil Mack Buffalo
7. Tampa Bay Buccaneers OT Greg Robinson Auburn
8. Minnesota Vikings OLB Anthony Barr UCLA
9. Buffalo Bills OT Jake Matthews Texas A&M
10. Detroit Lions CB Justin Gilbert Oklahoma State
11. Tennessee Titans ILB C.J. Mosley Alabama
12. New York Giants OT Taylor Lewan Michigan

Author's predictions

Jadeveon Clowney, DE, South Carolina

How many teams can possibly let Jadeveon Clowney slip between their fingertips?

For the Houston Texans, it makes sense to select a quarterback with No. 1 overall pick after last year's endless string of pick-sixes. The St. Louis Rams, at No. 2, already have Robert Quinn and Chris Long lined up at defensive end, so they're excused for taking Sammy Watkins, Greg Robinson or Jake Matthews.

Where should Jadeveon Clowney get drafted?

Submit Vote vote to see results

When the clock starts for the Jacksonville Jaguars at No. 3, they should not let the explosive defender fall any further.

The South Carolina stud was considered a future consensus No. 1 overall choice before his senior campaign, during which he recorded just three sacks for the Gamecocks. Then again, if you were playing a physical sport and knew an injury was the only thing blocking your path to millions of dollars, wouldn't you play at less than full throttle?

Physically speaking, Clowney has it all. Officially measured at 6'5" and 266 pounds, Clowney ran a sizzling 4.53 40-yard dash at the NFL Scouting Combine. He also completed 21 bench reps, which, according to ESPN Stats & Info, gave him the same results as another star.

While there are questions about his work ethic, NFL Media analyst Charley Casserly said on Path to the Draft that Clowney is too talented to pass up (via's Bryan Fischer):

What you want to do is when you wake up the next morning, feel good that you took the best player in the draft. The best talent in the draft is Jadeveon Clowney. Guy makes rare plays against the run, rare plays against the pass. Maybe the most talented defensive end I've ever scouted. There's a lot of questions to answer, but he's a rare talent at his position."

Jacksonville ranked 27th with 379.4 yards allowed per game and tied for last with 31 sacks. If Clowney is available, the Jaguars should waste little time in grabbing him.

Prediction: Jacksonville Jaguars (Pick No. 3)

Blake Bortles, QB, Central Florida

There's no consensus No. 1 quarterback in this draft, which means some wacky things could happen in the beginning.

This is an unusual draft, where as many as seven or eight guys can make a case for No. 1 consideration. Even if we establish that the Texans want a quarterback, that narrows the options down to three.

Which quarterback will have the best NFL career?

Submit Vote vote to see results

Blake Bortles is the exciting, trendy pick of the three. Johnny Manziel has been boxed into an easy villain narrative that fluctuates his draft projection wildly. Teddy Bridgewater, by contrast, is the boring selection with an accurate arm and higher floor.

That leaves us with Bortles, a junior from the relatively unknown Central Florida, who earned 9.4 yards per attempt while amassing 25 touchdown passes last year. At 6'5" and 232 pounds, he looks the part more than his peers, which is great for a team looking to cast a film about NFL stereotypes.

He boasts a Ben Roethlisberger build and a strong arm, which means the team that drafts him should be heavily invested in a vertical game. That sounds perfect at No. 5 for the Oakland Raiders, who clamor for gifted offensive athletes with size and speed.

They're known for taking big, fast wideouts such as Darrius Heyward-Bey, so why not target a passer with a cannon for an arm?

Prediction: Oakland Raiders (Pick No. 5)

Khalil Mack, DE/LB, Buffalo

Fair warning to everyone other than the Texans: Khalil Mack might not be available at your turn.

The Mack fan bus sells more seats by the day, and there probably won't be any tickets available by May. Two of its fans are highly influential analysts that could quickly sway public opinion.

Appearing on Minnesota's KFAN during the combine, NFL Media analyst Mike Mayock touted Mack as his No. 1 pick.

"He's explosive off the edge, he's tough, he's twitchy, he's got a little edge about him," Mayock said. "You talk about a kid like [Jadeveon] Clowney, who's just got superhuman abilities, versus this kid, and if I had a choice between the two, I think I'm taking Mack."

In his latest mock draft, ESPN's Mel Kiper Jr. jumped on board with Mack going No. 1.

The versatile Buffalo defender is earning rave reviews, but the allure of a fresh slate at quarterback and Clowney's sky-high upside will likely win out in the end. With passing dominating the league, Clemson's Sammy Watkins also warrants a top-five selection.

That leaves Mack on the board at No. 6, in which case Atlanta has no need to deliberate for the full 10 minutes.

The Falcons amassed 32 sacks last season while finishing 30th in Football Outsiders' DVOA. Mack shoots off the snap, whether in pursuit of the ball-carrier or pressuring the quarterback. He can deliver immediately for a team that nearly made the Super Bowl during the 2012 season.

Prediction: Atlanta Falcons (Pick No. 6)

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Liverpool Transfer News: Latest on Javier Mascherano, Emre Can, Yannick Bolasie

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Liverpool Transfer News: Latest on Javier Mascherano, Emre Can, Yannick Bolasie
David Ramos/Getty Images

Liverpool have plenty of preparation to do for next season. Brendan Rodgers' side will be confident of mounting another title challenge, but with Champions League football on the horizon, he needs to make vital signings ahead of a hectic schedule.

Javier Mascherano, Emre Can and Yannick Bolasie head the latest batch of transfer rumours. Here, we detail the latest news on all three.

Latest on Liverpool's Potential Signings

Javier Mascherano, Barcelona

Jon Super/Associated Press

Luis Enrique, Barcelona's new boss, has been quick to highlight Mascherano's importance since taking over from Gerardo Martino. The former Blaugrana captain indicated the Argentinian midfielder will take on a leadership role, noted by Dermot Corrigan of ESPN FC:

Sergi Font of Marca also believes Enrique told Mascherano "he is counting on him for next season," despite the player feeling "his time at Barcelona might have ended." Linked to Liverpool by Ben Jefferson of the Express, it seems there's plenty to be resolved before Mascherano's future becomes clear.

Walter Tamer, the player's agent, "is planning to come to Barcelona over the next few days," according to Font's report. Napoli president Aurelie De Laurentiis recently suggested the Italian side are "working on" a deal for the player, per Gazzetta dello Sport and via James Willoughby of, indicating it could be a long summer for those looking to land Mascherano's experienced talents.

Emre Can, Bayer Leverkusen

Rodgers is an avid developer of young talent, but his quest to sign Emre Can has always threatened to crumble at the will of Bayern Munich. Despite selling the 20-year-old midfielder to Leverkusen last summer, a pesky buy-back clause could see Liverpool's hopes of capturing the talent diminished, reported by Gary Jones of the Daily Star:

Liverpool are hoping their £10m bid will secure the deal, but are aware they could miss out to the German champs. Sources in Germany claim Bayern included a buy-back agreement in Emre's contract when he was sold to Leverkusen for £4.4m back in 2013.

The will of the player could decide this one. It's likely Can will want to make an impression in Bavaria if offered the opportunity to do so, having represented the club's youth ranks between 2009-2013. A German Under-21 international, the youngster may be inclined to continue learning at Leverkusen before returning to the Allianz Arena.

If Can wants to move to Liverpool, he must declare it now.

Yannick Bolasie, Crystal Palace

Clive Rose/Getty Images

Is Yannick Bolasie worth signing at £2.5 million?

Submit Vote vote to see results

Few Liverpool fans will have taken notice of Yannick Bolasie before their recent trip to Selhurst Park. The explosive winger ran riot as the Reds' 3-0 lead crumbled, but Rodgers may have seen it coming.

According to Adrian Kajumba of the Daily Star, the Liverpool boss is weighing up a cheap move for a player he has monitored throughout his career. "Rodgers is a long-term admirer of the £2.5m-rated midfielder going back to the days when he was in charge of Swansea and Bolasie was at Plymouth," noted Kajumba, who says Palace are "desperate" to keep their star in London.

Bolasie would certainly improve Liverpool's squad depth, offering an exciting option from the bench during what will be a busy 2014-15 season. Rodgers needs to up the output of his subs, as players including Iago Aspas, Luis Alberto and Fabio Borini have plenty to prove on Merseyside. Bolasie's fearlessness, and indeed versatility, fits into the manager's plans rather well.

Christopher Furlong/Getty Images

At such a cheap price, the Congo international is worth a shot. Liverpool's transfer activity is likely to be defined by a number of cheaper signings mixed with one or two more expensive investments, as Rodgers looks to build a squad that can compete across four fronts next season.

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