A better explanation of ribosomes:
As we have seen in the last few posts in this series, leaders in the Intelligent Design (ID) movement have developed an argument for design using the genetic code (the correspondences of amino acids and the nucleotide base triplets that specify them). Specifically, they claim that the genetic code is a “genuine code”—i.e. one constructed directly by an intelligent agent—and not a set of correspondences that arose through a natural process. As we have seen, however, this argument has to face strong evidence that part of the genetic code does in fact have its origin through physical interactions between amino acids and their corresponding codons or anticodons. The last post detailed how several amino acids do in fact directly bind to their own codons or anticodons—suggesting that the modern translation system, with its tRNA molecules that bridge amino acids and codons in the present day, is in fact the modified descendent of a translation system that relied on direct interactions. If so, the ID argument falls apart, and one of their major apologetic arguments is lost.
Previously, we saw that the main ID proponents who use the “genetic code is a real code” argument are Stephen Meyer and Paul Nelson. In their 2011 paper attempting to rebut the evidence for direct chemical binding between codons/anticodons and amino acids, one of their main lines of argument was that the observed binding was not genuine, but rather an artifact of poorly-designed experiments. While we have examined why this is not in fact the case for the experiments in question—they were done appropriately, and the results are not spurious—there is a second way to evaluate a body of scientific research done by one specific research group (in this case, the Yarus lab): look to see if it is profitably informing the research of other groups. If other groups are building on the work of another lab, and finding it to make accurate predictions, then we can be even more confident that the results are meaningful.
As the evidence mounted—through the work of Yarus and colleagues—that some amino acids do in fact bind their codons or anticodons, other researchers began to take note. One research group decided to use the results of the Yarus lab to make a prediction that could be tested by examining present-day proteins. They reasoned that if such interactions were important at the time when the translation process was emerging, that these same sorts of interactions may have been important for how complexes of proteins and RNAs worked together at that time. In other words, they reasoned that interactions between amino acids and codons/anticodons might have had other roles in addition to translation—perhaps structural roles. Proteins and RNAs that bound together to perform a function, for example, might have used these same chemical affinities to guide their formation. If so, then examining protein/RNA complexes that are old enough to date from this time in biological history might show evidence of close association between amino acids in the protein component and matching codons/anticodons in the RNA component. But where might an ancient complex of RNA and protein be found that could be used to test this prediction?
Ribosomes: a molecular time capsule
The obvious place to look was the ribosome—the very same RNA/protein complex that cells use for translation. Firstly, the ribosome can be found in all life in the present day, meaning that it is older than the proposed last universal common ancestor of all living things—or “LUCA” for short. As such, the ribosome would have been present at the time the current translation system was worked out. Secondly, the three-dimensional structure of the ribosome is known with great precision through a technique called X-ray crystallography. We know exactly how ribosomes, with their blend of RNA and protein components, are folded together. With these two features, looking at ribosomes was the perfect way to test the hypothesis that early RNA/protein complexes used chemical affinities between amino acids and their codons/anticodons for structural purposes as well as for translation.
The results, published in 2010, were striking. Within the folded structure of ribosomes, several amino acids were found in close association with some of their possible anticodons. Note that within a ribosome, the RNA components are not translated—they are untranslated RNA molecules that act as as a ribozyme, or RNA enzyme. The protein components come from different DNA sequences that are transcribed into RNA and then translated into protein before they join the ribosome complex. As such, the RNA components and the protein components of a ribosome are separate pieces—yet these proteins have some amino acids that are attracted to their anticodon sequences within the RNA components. So, even though these attractions are not useful for translation purposes, they are present within the ribosome structure. These results strongly support the hypothesis that interactions between amino acids and anticodons were biologically important at the time when translation emerged—since they are in large measure determining the three-dimensional structure of what is arguably the most important biochemical complex in life as we know it. Moreover, these results give strong experimental support for the idea that the genetic code was shaped by chemical interactions at its origin and is not a chemically arbitrary code. In response to these results, as well as the prior work by Yarus, a third research group has extended this type of analysis to the protein sets of entire organisms—and found that this pattern of correspondences between amino acids and their codons is widespread across whole genomes. This pattern—first identified by the Yarus group—has now been confirmed by the work of many other scientists, and it continues to make successful predictions.
A second observation from the ribosome study was also informative, but for a different reason. Some amino acids in the ribosome complex are closely associated with anticodons that do not, in the present-day genetic code, code for that amino acid. These anticodons, however, have previously been suspected to once have coded for those amino acids. The genetic code shows evidence of having been optimized through natural selection to minimize the effects of mutation. Such optimization requires some codon/anticodons to be reassigned to different amino acids over time. What was fascinating for the researchers looking at the ribosome was that some codons that were previously suspected to have been reassigned are associated with what were previously thought to be the “original” amino acid in the ribosome complex. This observation provides experimental support for codon reassignment over time: even though an amino acid and a particular codon/anticodon may have a chemical affinity for each other, this affinity could later be overridden by the introduction of tRNA molecules that bridge the amino acid and the codon without direct interaction between them. Despite this reassignment, the original correspondences remain in the ancient structure of the ribosome, where they serve a structural role. As such, this evidence is a window into how the genetic code may have evolved over time: starting with direct affinities, and then shifting to a modified system with tRNA molecules that allowed some of those original pairings to be shifted through natural selection.
In summary, the supposedly “flawed” work of Yarus (as claimed by Meyer and Nelson) is not only being used successfully by other researchers, those other researchers are adding to the evidence that the genetic code (a) has a chemical basis, and (b) has evolved over time. Both of these lines of evidence undermine the ID claim that the genetic code is an arbitrary code directly produced by a designer apart from a natural process.
In the next post in this series, we’ll move on to examining a second major claim of the ID movement as it pertains to biological information—that evolution cannot produce new information in the form of new proteins.
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Try not to forget that all aminos in life are ‘Left’ isomers.
This is impossible if there were even the slighest hint of randomness involved.
Ah, yes, the natural processor! My love, my love, my love is chemical.
All very imoressive and wordy - but that complex and critical coding that had to be in the first viable organism came about - how?
Please don’t tell me that random chance did it unless you’re willing to admit that you’ve never written computer code.
We know DNA has the following
1. Functional Information
2. Encoder
3. Error Correction
4. Decoder
These 4 items are basic and necessary. It is a closed system dependent on all operations to be functioning. You have information in a symbolic representation and a reading frame code. But beyond this, a formalization of semantic closure would need to be in place prior to the first cell. Put simply, a message assumes a protocol (agreement, set of rules) between the sender and the receiver, to help correctly encode and interpret the contents of the message. A simple example would be codons; they only represent amino acids if you have the system in place to interpret the functional relationship of the medium (aaRS). To state the obvious, this cannot just happen by accident.
Furthermore, the code and the functional information do not depend, in any way, from the chemistry which allows protein synthesis. Proof-reading, error-correction, editing and splicing, are not reducible to chemistry. Carrying out the genetic code is not reducible to chemistry. (Of course, they need that chemistry to work, but that is all another concept.)