RNA editing and Convergence, powerful evidence for design

1. Pretty easy for it to occur in an easy step. The reagents are all there anyway. RNAs are often autocatalytic. The only amazing thing is that RNA editing is not more widespread among the transcriptosome.and editing has many generalized properties that are merely chemistryBiol Chem. 2001 Aug;382(8):1147-56. Related Articles, LinksThis is the end: processing, editing and repair at the tRNA 3'-terminus.Schurer H, Schiffer S, Marchfelder A, Morl M.Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.The generation of a mature tRNA 3'-end is an important step in the processing pathways leading to functional tRNA molecules. While 5'-end processing by RNase P is similar in all organisms, generation of the mature 3'-terminus seems to be more variable and complex. The first step in this reaction is the removal of 3'-trailer sequences. In bacteria, this is a multistep process performed by endo- and exonucleases. In contrast, the majority of eukaryotes generate the mature tRNA 3'-end in a single step reaction, which consists of an endonucleolytic cut at the tRNA terminus. After removal of the 3'-trailer, a terminal CCA triplet has to be added to allow charging of the tRNA with its cognate amino acid. The enzyme catalyzing this reaction is tRNA nucleotidyltransferase, homologs of which have been found in representatives of all three kingdoms. Furthermore, in metazoan mitochondria, some genes encode 3'-terminally truncated tRNAs, which are restored in an editing reaction in order to yield functional tRNAs. Interestingly, this reaction is not restricted to distinct tRNAs, but seems to act on a variety of tRNA molecules and represents therefore a more general tRNA repair mechanism than a specialized editing reaction. In this review, the current knowledge about these crucial reactions is summarized.In some cases editing is a relic of the different origin of the mtDNA genomeJ Biol Chem. 1998 Nov 27;273(48):31977-84. Related Articles, LinksProcessing and editing of overlapping tRNAs in human mitochondria.Reichert A, Rothbauer U, Morl M.Max-Planck-Institute for Evolutionary Anthropology, Institute of Zoology, University of Munich, Luisenstrasse 14, 80333 Munich, Germany.Overlapping tRNA genes in mitochondria of many metazoans introduce a problem for the processing of such polycistronic primary transcripts. Using runoff transcripts and an S100 extract from HeLa cell mitochondria, the processing of the human mitochondrial tRNATyr/tRNACys precursor (carrying an overlap of one base) was investigated: tRNACys is released in its complete form carrying the overlapping residue at the first position, whereas tRNATyr lacks that nucleotide at the discriminator position. Partial deletion of tRNACys or complete replacement by a non-tRNA-like sequence does not alter the processing reaction and indicates that the upstream tRNATyr alone is recognized by a 3'-endonuclease activity. The truncated 3'-end of this tRNATyr is then completed in an editing reaction that incorporates the missing residue. The processing of this tRNA overlap seems to be species-specific, because an overlapping tRNA precursor (tRNASer(AGY)/tRNALeu(CUN)) from opossum mitochondria is not recognized by the human extract. Because processing activities for overlapping and nonoverlapping tRNA precursors could not be separated, it seems that one general activity is responsible for the 3'-end processing of mitochondrial tRNAs and that this activity coevolved with the particular overlap between tRNATyr and tRNACys in human mitochondria, being unable to recognize overlaps between other tRNAs.So programmed? Naahh...but if soWhat is the testable hypothesis of RNA editing being a program with a designed purpose? How could that be falsified? What is the evidence? How does it better explain the evidence than competing hypotheses?2.

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This is called convergence, something that is prevalent in nature and by its very definition is anti-evolutionary! (the word convergence is used to describe traits that cannot be attributed to common decent). Convergence is yet another signature God has left in his creation to thwart attempts to explain things via naturalistic processes.

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Man you are getting desperate with that last line....convergence is an evolutionary principle. There are only a limited number of ways to repair mRNA 3' ends thus the same mechanism will occur again and again. The mtDNA genome has a different origin than the nuclear genome and a vastly different repair enzyme milieu so of course the mechanisms of RNA editing in mtDNA will have an independent origin...how you leap to this as evidence god, gods, tooth fairies is really baffling.oops..missed this one...and it does not even rely on convergence...FEBS Lett. 1997 Jun 16;409(3):320-4. Related Articles, LinksRNA editing in metazoan mitochondria: staying fit without sex.Borner GV, Yokobori S, Morl M, Dorner M, Paabo S.Institute of Zoology, University of Munich, Germany.RNA editing subsumes a number of functionally different mechanisms which have in common that they change the nucleotide sequence of RNA transcripts such that they become different from what would conventionally be predicted from their gene sequences. RNA editing has now been found in the organelles of numerous organisms as well as in a few nuclear transcripts. Most recently, it was shown to affect tRNAs in the mitochondria of several animals. The occurrence and evolutionary persistence of RNA editing is perplexing since backmutations in the genes might be assumed rapidly to eliminate the need for 'correction' of the gene sequences at the post-transcriptional level. Here, we review the recent RNA editing systems discovered in animal mitochondria and propose that they have arisen as a mechanism counteracting the accumulation of mutations that occurs in asexual genetic system.[This message has been edited by Mammuthus, 09-09-2003]

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Easy. Produce one example of a program (code) arising via a naturalistic process, and the claim would immediately be falsified. Just find one counter-example.

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First, you cannot even define a code properly as seen in the information and genetics thread and you dismiss any evidence that contradicts your assertion regardless of its merits. In any case, you can always just say it was still designed as you have done. But how do you test for design. If you define anything that is a complex molecule or a complex pattern as a result of intelligence, snowflakes for example, even if you see the snowflake form you can still say the designer did it but we could not see it...there is no way to falsify it and it is therefore a supernatural explanation and non-scientific.I can synthesize random DNA sequences, replicate them, and transform DNA in the lab using all naturally occurring reagents and chemical systems that are naturally occurring put it in bacteria or fruit flies and watch it evolve over generations into a different sequence...so naturally occurring information that can occur in the lab and in nature without intelligence...but this does not falsify ID because you can still always say the pink unicorn did it...and whereas I can make observations and do lab experiments to show evolution by natural selection...what experiment can you propose to show that my bacteria has acquired antibiotics resistance due to gods intervention?

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Now, I would ask that you provide a testable hypothesis of RNA editing being a program that arose naturalistically. How could that be falsified?

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are you asking me precise details on a testable hypothesis of the very first RNA editing system or the inheritance of RNA editing mechanisms by common descent which PaulK addressed? I ask because it will determine how I answer and support what I say.

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Is convergence anti-common decent or not. Yes or no.

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No to anti-common descent but yes to inheritance of a specific trait i.e. the same mutation occurring independently. Horizontal transfer is another example. Bacterial conjugation and transfer of antibiotics is another example..hardly a new finding or an overturun of genetics or evolution. If two people have different mutations in the dystrophin gene in two independent families and the children as a result have muscular dytrophy, does this violate common descent? Are the children not related to their parents?See below, random mutation can affect the same genes and result in the same mutations/phenotypes without violating common descent.Nature. 2003 Aug 21;424(6951):935-8. Related Articles, LinksComment in:
Nature. 2003 Aug 21;424(6951):894-5.Regulatory evolution of shavenbaby/ovo underlies multiple cases of morphological parallelism.Sucena E, Delon I, Jones I, Payre F, Stern DL.Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey 08544, USA.Cases of convergent evolution that involve changes in the same developmental pathway, called parallelism, provide evidence that a limited number of developmental changes are available to evolve a particular phenotype. To our knowledge, in no case are the genetic changes underlying morphological convergence understood. However, morphological convergence is not generally assumed to imply developmental parallelism. Here we investigate a case of convergence of larval morphology in insects and show that the loss of particular trichomes, observed in one species of the Drosophila melanogaster species group, has independently evolved multiple times in the distantly related D. virilis species group. We present genetic and gene expression data showing that regulatory changes of the shavenbaby/ovo (svb/ovo) gene underlie all independent cases of this morphological convergence. Our results indicate that some developmental regulators might preferentially accumulate evolutionary changes and that morphological parallelism might therefore be more common than previously appreciated.this toNature. 1989 Aug 10;340(6233):465-7. Related Articles, LinksDNA phylogeny of the extinct marsupial wolf.Thomas RH, Schaffner W, Wilson AC, Paabo S.Department of Biochemistry, University of California, Berkeley 94720.The phylogenetic affiliation of the extinct marsupial wolf (Thylacinus cynocephalus), which once was widespread in Australia, has been uncertain. On the basis of morphology, some systematists argue that the thylacine was most closely related to an extinct group of South American carnivorous marsupials, the borhyaenids, whereas others consider it to be closer to Australian carnivorous marsupials. Here we use direct sequencing by means of the polymerase chain reaction (PCR) to compare 219 bases of mitochondrial (mt) DNA from museum specimens of the marsupial wolf and representatives of six genera of extant marsupials. In agreement with the results of an antigenic study of albumin, our genetic data suggest that the marsupial wolf was more closely related to other Australian marsupial carnivores than to those of South America. Thus, the marsupial wolf represents an example of convergent morphological evolution to South American carnivorous marsupials as well as to true wolves.Here is another example where there is strong selection for a characteristic that puts a constraint on the entire system an lo and behold, similar systems evolve under these constraints...wow..what a discovery Proc Natl Acad Sci U S A. 2003 Feb 4;100(3):1072-7. Epub 2003 Jan 21. Related Articles, LinksParallel changes in gene expression after 20,000 generations of evolution in Escherichiacoli.Cooper TF, Rozen DE, Lenski RE.Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA. cooperti@msu.eduTwelve populations of Escherichia coli, derived from a common ancestor, evolved in a glucose-limited medium for 20,000 generations. Here we use DNA expression arrays to examine whether gene-expression profiles in two populations evolved in parallel, which would indicate adaptation, and to gain insight into the mechanisms underlying their adaptation. We compared the expression profile of the ancestor to that of clones sampled from both populations after 20,000 generations. The expression of 59 genes had changed significantly in both populations. Remarkably, all 59 were changed in the same direction relative to the ancestor. Many of these genes were members of the cAMP-cAMP receptor protein (CRP) and guanosine tetraphosphate (ppGpp) regulons. Sequencing of several genes controlling the effectors of these regulons found a nonsynonymous mutation in spoT in one population. Moving this mutation into the ancestral background showed that it increased fitness and produced many of the expression changes manifest after 20,000 generations. The same mutation had no effect on fitness when introduced into the other evolved population, indicating that a mutation of similar effect was present already. Our study demonstrates the utility of expression arrays for addressing evolutionary issues including the quantitative measurement of parallel evolution in independent lineages and the identification of beneficial mutations.You harp on this topic often but it is not exactly a complicated concept.

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Following multiple similar paths through random copy mistakes and blind selection? You sure have a lot of faith.

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hardly faith...a lot of work has been done on RNA editing. tRNA secondary structure is well characterized, overlapping genes have been known for decades, RNA editing enzymes have been purified and characterized, so the constraints on editing systems are pretty well understood though not fully...knowing those constraints on what is or what is not realistic for editing and then seeing a common features in RNA editing in nature is hardly rocket science and does not require one to invoke never ever seen, zero evidence for, non testable non falisfiable pink unicorns up in the sky..

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Unfortunately I only have time for one post today (I have a self-imposed rule that I will not post from home, let alone even look at a discussion board — so far so good).

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Thats funny Fred, I have a similar self imposed rule...I also try to enforce a "no EvCforum on the weekends" rule...though I sometimes slip....what do you know, convergence

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I ask again, is convergence antithetical to common decent? If you answer no, how do you explain this in light of Campbell’s statement above?

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Simple, like with horizontal gene transfer or bacterial conjugation, there are similar traits that can be acquired by mechanisms other than inheriting a copy from your parents. If you have a retroviral infection and a copy integrates in your germline i.e. sperm, you can pass that integrated provirus to you children and they can pass it on etc. etc. even though you did not inherit that virus from your parents...8-9% of the human genome is made of elements of this kind called human endogenous retroviruses (HERVs). This still does not violate common descent of the host organism with its last common ancestor any more than you having a novel proviral integration suggests your parents are not related to you.Similarly for convergent traits, read the thylacine wolf article I posted. Similar ecological niche as canids and some similarities in morphology. But DNA analysis shows it is a marsupial with no affinity to canids. This hardly violates common descent.

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Would you at least agree it disrupts evolutionist efforts to construct phylogenies

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Yes, I would agree that it has disrupted phylogenetics. However, now that phylogenetics is more and more based on genomics, a lot of relationships among groups are becoming much clearer since usually even if the morphology has converged, the neutral DNA markers used to test phylogenetic associations have not.Would you at least agree it disrupts evolutionist efforts to construct phylogenies? [/quote]

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Since people are fond of citing logical fallacies on this board, in this case this is the fallacy of the exceptions prove the rule (can’t remember the technical, literature geek name). Horizontal gene transfer doesn’t even touch the tip of the iceberg of the myriad of examples of convergence in nature.

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Then I guess you do not believe in mendelian genetics or heredity either as the findings of horizontal transfer is actually more of a problem for Mendel's original laws than Darwin's theory. But you have it completely backwards. The discovery of bacterial conjugation, horizontal transfer, convergent evolution all strengthened both genetics and evolution because it explained occurrences that were previously exception to the rule and clarified the mechanism.

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I’m glad you at least acknowledge that convergence disrupts scientist’s ability to construct phylogenies. Evolution certainly never predicted that nature would be chalked full of them, the theory sure would have been better off without them (seems to be a common theme of the theory, things always point against it! ). The excuse you give however smells like a circular argument to me. But I’ll have to wait and see.

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Not sure what you mean here. If I have a phylogeny based solely on morphology that shows that the thylacine wolf occupies a near identical niche to that of canid wolves and is morphologically very similar, I then analyze its DNA and see that all genetic markers show conclusively it is a marsupial with no relationship to canids...why is this a problem for evolution? I can see where it is a problem for the phylogenetics of this species group and can see that duh! not all markers are useful for specific analysis which is known from genetics, forensics, population biology, ecology you name it....so?There is a little thing that is foreign to religion but is key to science..it is called progress. Over time, science improves itself and thus exposes problems with past work. Religion on the other hand denies, covers up, or just mistranslates its texts into another language and then back again to cover up fallacies without ever progressing...it is not circular reasoning.