First the new finding: Summary and the actual paper.
Now, consider this snippet from that brochure, especially the bold emphasis I've added (pages 5-7):
Of course there are some semantic and red-herring issues when it comes to how JWs use the phrase "by chance" in their publications. Evolution isn't merely by chance, that's just half the, it's rather by the non-chance selection of chance mutations. For example the paper I've linked to even addressing this when talking about the odds of their finding happening by chance:Researchers have learned that for a cell to survive, at least three different types of complex molecules must work together—DNA (deoxyribonucleic acid), RNA (ribonucleic acid), and proteins. Today, few scientists would assert that a complete living cell suddenly formed by chance from a mix of inanimate chemicals. What, though, is the probability that RNA or proteins could form by chance?*
Many scientists feel that life could arise by chance because of an experiment first conducted in 1953. In that year, Stanley L. Miller was able to produce some amino acids, the chemical building blocks of proteins, by discharging electricity into a mixture of gases that was thought to represent the atmosphere of primitive earth. Since then, amino acids have also been found in a meteorite. Do these findings mean that all the basic building blocks of life could easily be produced by chance?
“Some writers,” says Robert Shapiro, professor emeritus of chemistry at New York University, “have presumed that all life’s building blocks could be formed with ease in Miller-type experiments and were present in meteorites. This is not the case.”2*
Consider the RNA molecule. It is constructed of smaller molecules called nucleotides. A nucleotide is a different molecule from an amino acid and is only slightly more complex. Shapiro says that “no nucleotides of any kind have been reported as products of spark-discharge experiments or in studies of meteorites.”3 He further states that the probability of a self-replicating RNA molecule randomly assembling from a pool of chemical building blocks “is so vanishingly small that its happening even once anywhere in the visible universe would count as a piece of exceptional good luck.”4
What about protein molecules? They can be made from as few as 50 or as many as several thousand amino acids bound together in a highly specific order. The average functional protein in a “simple” cell contains 200 amino acids. Even in those cells, there are thousands of different types of proteins. The probability that just one protein containing only 100 amino acids could ever randomly form on earth has been calculated to be about one chance in a million billion.
Researcher Hubert P. Yockey, who supports the teaching of evolution, goes further. He says: “It is impossible that the origin of life was ‘proteins first.’”5 RNA is required to make proteins, yet proteins are involved in the production of RNA. What if, despite the extremely small odds, both proteins and RNA molecules did appear by chance in the same place at the same time? How likely would it be for them to cooperate to form a self-replicating, self-sustaining type of life? “The probability of this happening by chance (given a random mixture of proteins and RNA) seems astronomically low,” says Dr. Carol Cleland*, a member of the National Aeronautics and Space Administration’s Astrobiology Institute. “Yet,” she continues, “most researchers seem to assume that if they can make sense of the independent production of proteins and RNA under natural primordial conditions, the coordination will somehow take care of itself.” Regarding the current theories of how these building blocks of life could have arisen by chance, she says: “None of them have provided us with a very satisfying story about how this happened.”6
[E]ven if one were to deny all of these arguments and assert that our findings could be due to chance, chance does not obviate the observation that tRNA appear to be encoded in rRNA, that rRNA may have been the evolutionary source of tRNA or that tRNA may have, conversely, given to rRNA. Evolution works by chance. The issue is not whether the appearance of tRNA in rRNA is by chance, but whether there was selection for such chance events that has caused these homologies to be retained through evolution and we claim there was because of additional data we offer concerning the unusually high degree of active site protein modules associated with ribosome function that are also encoded in the rRNA.
Anyway, this new paper has some interesting tidbits among other more important things (such as putting forth the selfish ribosome model as opposed to selfish gene model). For example, when it comes to RNA molecules and Proteins cooperating for self-replication the paper says:
In short, two conclusions are inescapable. First, the ribosome-related information encoded in rRNA is extremely dense—so dense as to make it extremely likely that extensive selection over a very long geological period of time must have been at work to incorporate its many facets. rRNA appears to have been used evolutionarily as structural components of the ribosomes themselves; as tRNAs to translate the sequences; as mRNAs, using all possible reading frames, to encode key ribosomal proteins; and it is also highly redundant, encoding some functional elements such as tRNAs, polymerases and ligases in multiple ways. A second conclusion is that rRNA specifically encodes molecules associated with functions that could potentially have permitted a primitive ribosome to reproduce itself. The fact that all of this information resides in the ribosomes of present-day E. coli (and other bacterial) species must be considered in light of several billion years of evolution that have occurred since ribosomes were incorporated into cells. The remaining homologies are almost certainly vestigial and represent fragments remaining after gene loss or transfer to the cellular genome. Thus, the primordial ribosome may have been more complex or complete than that represented by our search strategy.
Another likely implication of our results is that RNA co-evolved with proteins to yield a self-organizing, self-replicating entity. Given the high information density found in the ribosome, selection is likely to have been for peptides that could bind to the RNA sequences encoding them (i.e., for molecular complementarity) and the resulting RNA-peptide interactions would additionally have been selected for their functions (ability to form platforms that bound other RNA sequences; promoted peptide formation; had RNA or DNA polymerase or ligase activity; stabilized RNA and/or peptides against degradation; etc.) (Hunding et al., 2006 and Root-Bernstein and Dillon, 1997). Prebiotic tRNAs, for example, may not have been just tRNAs, but also mRNAs that encoded crucial peptide sequences with various enzyme or structural functions that were enhanced by binding to their own, or other tRNA sequences. Specialization of RNA into ribosomal, messenger and transfer types likely came later in evolution.