Literature

The translation of mRNA into protein "occurs on one of nature's most versatile molecular synthesizers: the ribosome." The analogy for this machine in the human world is the factory: the mass production line from which emerges a stream of products. However, the factory is not like a Fordist assembly line, with lots of workstations, but more like an Advanced Manufacturing Technology cell, where all the instructions are digital and where the machinery translates information into a physical product.
"In the past decade or so, the ribosome has gone from being a biomolecule whose very structure was largely a mystery to one whose architecture is known at an atomic level and whose detailed workings are beginning to be better understood." The fruits of this research are to be found in a variety of formats, including some remarkable simulations, such as here. The most favoured model for the working of ribosomes involves the "proton-shuttle mechanism".
"Computation and simulation are likely to be extraordinarily useful for further clarifying the ribosome's mechanism", because nothing else approaches being able to capture the molecular-level motions and chemical reactions. One recent study is described as "the largest simulation performed to date in biology."
One researcher has commented: "at this point, in spite of high-resolution crystal structures and decades of biochemical, genetic, and biophysical studies, I don't think we understand the fundamental mechanisms at all." Another says: "Where one person says we have the answers, the next person says we have the questions."

So how should we approach the next phase of research into this "huge complex of protein and RNA with a practical and life-affirming purpose-catalyzing protein synthesis"? Without ribosomes, DNA and mRNA are destined to degradation. Like a human factory, information by itself is necessary by not sufficient. The ribosome is a super-machine, not a basic tool. The bacterium E. coli has a ribosome made-up of 50 proteins, each of which requires manufacturing prior to assembly. This is the old "which came first: the chicken or the egg?" conundrum. It is a major challenge for abiogenesis, which is still dabbling with organic chemistry and is not within sight of a working cell (the only environment that can be deemed stable for any possible precursor molecules).
The day is coming when biologists will look at the animations of the ribosome and say: "Why did we resist considering the design inference for so long?"

Protein Factory Reveals Its Secrets
Stu Borman
Chemical & Engineering News, 19 February 2007

Last year, the Nobel Prize in Chemistry heralded work on DNA transcription, a cornerstone process in molecular biology in which a cell synthesizes a messenger RNA (mRNA) version of genomic DNA. For some time, many research teams have been studying the other side of molecular biology's central dogma - the translation of mRNA into protein. That translation occurs on one of nature's most versatile molecular synthesizers: the ribosome. [snip]

Translation Movie shows the process of mRNA-to-protein translation, including initiation, protein chain elongation, and termination.