Figure 4. Position of RP L9, L19, L25, L30, L34 and L36 in the LSU of the ribosome of E. coli
(Article image and caption.)
Posted on 11/30/2018 8:22:36 AM PST by fishtank
The irreducibly complex ribosome is a unique creation in the three domains of life
by Matyas Cserhati and Warren Shipton
The evolution of the genetic code and the ribosome are intimately connected as the code is expressed through ribosomal activity. Models of genetic code evolution are analyzed. The error-minimization theory is faulty in that it supposes that highly error-prone genetic codes could produce more precise codes over time. The stereochemical theory posits complementarity between nucleotides and amino acids, but cannot demonstrate this for the whole code. The co-evolution theory states that the genetic code developed from an ancestral through an ancient to a modern state. There is no evidence for ancestral code protein generation. The big question remains why the code solidified in its present state. Finally, the accretion theory of ribosomal evolution is shown incapable of answering key questions.
(Excerpt) Read more at creation.com ...
Figure 4. Position of RP L9, L19, L25, L30, L34 and L36 in the LSU of the ribosome of E. coli
(Article image and caption.)
I think that proves Russian collusion.
This is over my head, but it sure looks like the extreme complexity cannot be explained by things coming together randomly.
Before I could even pass through the threshold of this discussion, I stumbled on the word ‘irreducibly’ at the doorway.
Irreducibly means something that cannot be made smaller, simpler or further diminished. “This is as good as it gets!”
Where is that guy with the uncombed hair and 70’s suit saying: “I’m not saying it IS Aliens...But....It’s Aliens!”
Turtle sitting on top of a fence post
Looks like a sideways Christmas tree.
More importantly, an irreducible structure serves no purpose if any component is removed (or not yet installed)... Random genetic mutation can’t “forsee” the needed components and assemble them later. Evolution without the guiding hand of a Creator is bunkum.
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.
bmp
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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.
"Absence of evidence is not evidence of absence."
The big question remains why the code solidified in its present state.
Yep, that remains a good question (if, indeed, it has "solidified" - something tells me that that isn't a very rigorous word in evolutionary biology circles). No doubt scientists (not fortune-tellers) are working on it right now.
Finally, the accretion theory of ribosomal evolution is shown incapable of answering key questions.
Then I guess a wizard did it! Seriously: Anyone got a better verifiable theory? Bring it on!
Regards,
.
>> “but it sure looks like the extreme complexity cannot be explained by things coming together randomly.” <<
No kidding!
.
“It is evident that ribosomes are prerequisites to the life of the cell in that they convert genetic information into functional proteins.“
Ribosomes ARE proteins. Therefore, there must have been a way to make proteins before ribosomes existed.
“It is a paradox of evolution that the composition of the prokaryotic ribosome is different to that of the eukaryotic one, yet the ribosome has supposedly evolved through a number of intermediary steps back into a ribosome”
Similar results staring from slightly different origins is pretty common in biology.
“The theory naturally cannot carry much weight, since if the translation machinery is so error-prone to begin with, no meaningful proteins can come from such a configuration. Errors only lead to more errors, not higher precision, which requires intelligent input. From a thermodynamic viewpoint, disorder only increases as mutations accrue.”
Natural selection weeds out unfavorable mutations and promotes successful ones. Thermodynamics has nothing to do with this as energy is constantly added to the system.
“Why don’t we find any protein sequences in the fossils of ancient organisms, which only have primary amino acids? ”
We don’t find any protein sequences in ancient fossils.
“We only find proteins made up of all 20 amino acids. Why didn’t the genetic code keep on expanding to cover more than 20 amino acids? ”
Twenty works good enough, but obviously there was no overall advantage in more than twenty.
And so on.
Deo Gratias!
All I know is that if we discovered a planet full of robots coded with an operating system that gave them intelligence and dynamic adaptation, along with the ability to self-replicate, we probably wouldn’t think: “wow, this operating system wrote itself!”.
Just give the two manmade gods of time and chance ( whatever those are) to make it all come out right.
Atoms and molecules don’t behave randomly.
For those that want to help out science, please consider donating to the Folding@Home project contributing to original research in genetics.
The FreeRepublic F@H started out ~2001 and grew to over 500 daily contributors and 1800 systems contributed. We have slowly dropped contributors, due to a lack of marketing and competition from block chain mining.
However our folks now contribute more points per day (PPD) than all 500 of us back then. We have consistently stayed around the #100 team in the world. By comparison, DU has dropped to about #700 and now has one contributor.
Blessings!
Ah, yes, the natural processor! My love, my love, my love is chemical.
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