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Member (Idle past 4855 days) Posts: 310 From: Broomfield Joined: |
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Author | Topic: RNA editing and Convergence, powerful evidence for design | |||||||||||||||||||||||||||||||||||
Fred Williams Member (Idle past 4855 days) Posts: 310 From: Broomfield Joined: |
Recently Mammuthus cited the following interesting article:
quote: I haven’t had the opportunity to track down the full article, but it appears that much can be gleaned from the abstract. Several provide strong arguments for design: 1) The article properly describes ‘RNA editing’ as a programmed alteration (emphasis mine). We have discussed this quite a bit, and I would like to hear evolutionists explain how such a program (or code) can evolve through small, incremental steps. 2) The authors note that particular RNA editing systems display a narrow phylogenetic distribution, which argues that such systems are derived within specific eukaryotic lineages, rather than representing traits that ultimately trace to a common ancestor of eukaryotes, or even further back in evolution. (emphasis mine). In other words, they can’t find a common ancestry thread so they have to rely on the independent evolution of these complex RNA editing systems! (how many seperate, independent paths of evolution of RNA editing the authors believe occurred cannot be gleaned from the abstract) 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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PaulK Member Posts: 17822 Joined: Member Rating: 2.2 |
1) Without seeing what the "programmed" means in context arguing that it is evidence for design or not is premature.
2) The fact that these mechanisms are narrowly confined phylogenetically is evidence for common descent and therefore FOR evolution. And there is no reason to conclude that simple convergence indicates design - usually it indicates that a narrow range of available solutions to a particular problem (e.g. sharks, icthyosaurs and dolphins have similar form because they have similar lifestyles),
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Rei Member (Idle past 7012 days) Posts: 1546 From: Iowa City, IA Joined: |
You're just latching onto the word "programmed". Did you read the context? They're using "programmed" in the meaning of "preset" - i.e., it follows a specific set of rules. So? That's the same as saying that platinum does a "programmed" modification of petroleum. I'm sure that the author would be quite upset with you abusing their choice of language this way.
PaulK already did my answer for #2 - it's quite obvious to any evolutionist that this is to be *expected*. Only the descendants of an organism which gain a mutation inherit its abilities. In short, this article appears to be about a rather peculiar approach some branches of organisms took towards increasing the number of proteins they can make - which in some cases may prove to be a selective advantage. There's nothing, from what is in this article, inherently difficult about RNA gaining this ability - it would have been mentioned if there was, and I can't picture why there would be. If a molecule can catalyze reactions other molecules given proper conditions, why can't it cause itself to react given proper conditions? ------------------"Illuminant light, illuminate me."
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Mammuthus Member (Idle past 6475 days) Posts: 3085 From: Munich, Germany Joined: |
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 chemistry Biol Chem. 2001 Aug;382(8):1147-56. Related Articles, Links This 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 genome J Biol Chem. 1998 Nov 27;273(48):31977-84. Related Articles, Links Processing 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 so What 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. quote: 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, Links RNA 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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Fred Williams Member (Idle past 4855 days) Posts: 310 From: Broomfield Joined: |
quote: 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. Now, I would ask that you provide a testable hypothesis of RNA editing being a program that arose naturalistically. How could that be falsified?
quote: Is convergence anti-common decent or not. Yes or no.
quote: Following multiple similar paths through random copy mistakes and blind selection? You sure have a lot of faith.
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PaulK Member Posts: 17822 Joined: Member Rating: 2.2 |
As I pointed out the convergence in THIS case is definitely NOT anti-common descent.
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Fred Williams Member (Idle past 4855 days) Posts: 310 From: Broomfield Joined: |
quote: You have not made a case for this, nor does Mammuthus seem to agree with you since he is defending it as convergence. Mammuthus? In a previous thread where RNA editing first came up I asked Mammuthus if this was convergence and he didn't reply (I don't think it was intentional, he just missed it). This was one of the primary reasons I started this thread, to get to the bottom of this. Now Mammuthus is defending it as convergence, and you are saying it isn't. I only have the abstract to go by since obtaining the full article will not be convenient for me. I am more than willing to drop the claim of convergence if it can be shown from the article that it is not convergence. So far you are the only one interpreting the abstract as non-convergence, and your reasons are, so far, not even remotely convincing.
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Adminnemooseus Administrator Posts: 3974 Joined: |
Thread moved here from the Evolution forum.
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PaulK Member Posts: 17822 Joined: Member Rating: 2.2 |
Well if we are going to talk about whether a case has been made - where's yours ?
Come to that if you think that I am denying that this is convergence have you actually read either of my posts ? I never said that - what I do deny is that convergence is automatically evidence against common descent and that in this case the evidence supports common descent. Since you can't fill in the dots in my argument as to why it supports common descent here it is:The particular implementations of RNA editing have a narrow phylogentic distribution. This is what we would expect if they arose independantly and were transmitted by common descent. Design does not have the limitations of common descent and could produce any distribution at all. Therefore the fact that we find a distribution compatible with common descent is evidence for common descent. Now perhjaps you would like to produce a similarly detailed argument for why you think this is somehow evidence AGAINST common descent.
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Mammuthus Member (Idle past 6475 days) Posts: 3085 From: Munich, Germany Joined: |
quote: 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?
quote: 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.
quote: 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, Links Comment 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 to Nature. 1989 Aug 10;340(6233):465-7. Related Articles, Links DNA 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, Links Parallel 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.edu Twelve 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.
quote: 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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Zealot Inactive Member |
Hi, I think Fred might be referring to the article 'Evolution returns to the same genes again and again', taken from the NewScientist 23rd August Page 15.
Which was from Nature vol 424 p 931.MK Rich Ardson - MK Blog Rich under 'Hotspots for evolution' thought it might help.
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Peter Member (Idle past 1478 days) Posts: 2161 From: Cambridgeshire, UK. Joined: |
Convergence of any kind is not contrary to evolution,
nor does it make any comment on common descent. Convergence is about the existence of similar propertiesthat come about via differing mechanisms. Common descent is about the same property by the same mechanismbeing exhibited in different types of organism. Both are explainable within the evolutionary paradigm.
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Peter Member (Idle past 1478 days) Posts: 2161 From: Cambridgeshire, UK. Joined: |
Show me that DNA/RNA chemical systems a genuine codes first.
If they are not then the whole line fo argument fails. It's just chemistry -- albeit highly complex in terms orinteractions.
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Fred Williams Member (Idle past 4855 days) Posts: 310 From: Broomfield Joined: |
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).
Peter, Paul, and Mary, er, I mean Mammuthus all appear to be saying that convergence is not used as an explanation of traits that cannot be attributed to common decent. Here’s what my College Biology books says: There is a wild card in this game of making evolutionary connections by evaluating similarity: Not all likeness is inherited from a common ancestor. Species from different evolutionary branches may come to resemble one another if they have similar ecological roles and natural selection has shaped analogous adaptations. This is called convergent evolution, and similarity due to convergence is termed analogy, not homology - Campbell, Reece, Mitchell, Biology 5th Edition, 1999 (emphasis in original) 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? Would you at least agree it disrupts evolutionist efforts to construct phylogenies?
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Loudmouth Inactive Member |
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? Would you at least agree it disrupts evolutionist efforts to construct phylogenies?
Anthithetical: no. Campbell's statement was stating unreliability of using similar morphology as the ONLY criteria for phylogenies. One must also consider geographic isolation and fossil intermediates from separate common ancestors. The use of genetic similarity and markers are also very useful in determining if convergent evolution occurred. For instance, if you ask four friends to meet you at the town square and each friend lives on opposite sides of town, would you assume they took the same route to reach the town square? Convergent evolution describes different phylogenies that are originially morphologically different but become similar due to similar niche pressures. If design were an element, analogous functions would have analagous genetics. But in fact the opposite is true. Solutions to a problem give rise to similar function but genetically different pathways along lines that support a common ancestor.
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