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Problems for evolution — squid recodes its own RNA

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  • Originally posted by User Name View Post
    I think it has evolved into a movement where you just tack "God did it" onto anything in science that is not currently explained entirely through natural processes, rather than remaining strictly a YEC model of "God did it".



    I hope y'all caught the strategic use of the word "evolved" there.
    Militant Moderate

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    • Originally posted by User Name View Post
      The Discovery Institute may not frequently publish anti-YEC articles as does Biologos, but the DI apparently does actively oppose YE creationism; see this link for example:

      http://www.evolutionnews.org/2012/02...i_1055841.html
      Where you going to with the goal posts? It doesn't matter if anyone publishes anti-YEC material. What I said though is that Biologos publishes anti- christian material. I suggested you look at the thread on that topic. They have had writers all but admit they pose as Christians...and admit their teaching drives people from the church.
      Without Genesis, absolutely nothing makes sense in all of Scripture.

      Comment


      • kdhall
        Where is the evidence for a global flood?
        E≈mc2
        "the best maths don't need no stinkin' numbers"

        "The waters under the 'expanse' were under the crust."
        -Bob B.

        Comment


        • Denny wrote, earlier:
          Here's just two of the things you 'forgot to include' Professor Stripe:
          "We have demonstrated that RNA editing is a major player in genetic information processing rather than an exception to the rule," said Dr. Eisenberg. "By showing that the squid's RNA-editing dramatically reshaped its entire proteome -- the entire set of proteins expressed by a genome, cell, tissue, or organism at a certain time -- we proved that an organism's self-editing of mRNA is a critical evolutionary and adaptive force."

          "The principle of adaptation -- the gradual modification of a species' structures and features -- is one of the pillars of evolution. While there exists ample evidence to support the slow, ongoing process that alters the genetic makeup of a species, scientists could only suspect that there were also organisms capable of transforming themselves ad hoc to adjust to changing conditions. (Emphasis added.)"

          So the scientists were expecting to find animals like this at some point, the study doesn't discredit evolution in the slightest [It actually credits this new discovery with proving mRNA editing as crucial to evolution in the bold font above], and the study says that both evolution and adaptation (STRIPE BELIEVES IN NEITHER) are supported by "ample evidence."

          Congratulations Stripe! You just disproved everything you have been saying on other related threads.


          Did you think no one would notice what you deleted, Stipe?
          This message is hidden because ...

          Comment


          • How can something be part of a "biblical model" if it isn't in the Bible?
            The "biblical model" doesn't have much to do with the Bible.
            This message is hidden because ...

            Comment


            • Originally posted by 6days View Post
              Adaptation is a 'piller' of Biblical creation also.
              And where is the Biblical justification for that?

              6days, "adaptation" is an ad hoc hypothesis to try to save creationism from falsification. Creationists could not deny all the observed examples of adaptation over generations. What they tried to do is say "adaptation within limits" of a "kind".

              Problem for evolutionists is they believe in gradual modification. There are numerous examples of rapid change...rapid adaptation. Evidence supports... "In the beginning, God created..."
              That is a strawman. First you need to define "gradual". Then you need to define "adaptation".

              "Many species once formed never undergo any further change, but become extinct without leaving modified descendants; and the periods, during which species have undergone modification, though long as measured by years, have probably been short in comparison with the periods during which they retain the same form." Charles Darwin, Origin of Species, 4th and later editions, pg. 408-409

              Notice in this article that the squids are NOT modifying their DNA. Instead, they are modifying the proteins by editing the mRNA. In particular, mRNA is made in exons, and there are proteins that modify which exons, and in which order, are converted to proteins. The proteins that do that are, themselves, coded by DNA. Thus, those proteins have evolved over generations.
              If sound science appears to contradict the Bible, we may be sure that it is our interpretation of the Bible that is at fault." Christian Observer, 1832, pg. 437

              Comment


              • Originally posted by 6days View Post
                You are getting silly now. Our argument in this thread is that mutations and selection don't, and can't account for the various kinds of animals. Observable science shows how organisms adapt...and often rapidly. *Your belief system requires you to believe in the unobservable.*
                What the article showed is that information is processed at mRNA level before it is translated to proteins. Not that big a deal. After all, information is introduced by the folding of the proteins after then come out of the ribosomes. Specific proteins (themselves coded by DNA) called chaperones do this. Also, proteins are glycosylated after synthesis, and in may cases (like proteoglycans), this is essential to their function. Again, the glycosylation is by other proteins, themselves coded by DNA. Some proteins, like HSP90, even determine which isomers of proteins will be transcribed to mRNA. HSP90 is reactive to the environment, but it itself is coded by DNA so it has evolved to do its job.

                Now, if mutation and selection cannot account for the diversity of organisms, then there would be independent DNA sequences in different "kinds" of organisms. OTOH, if mutation and selection do account for organisms, their DNA sequences will show patterns of inheritance (from those mutations and selection of an original in the common ancestor). DNA sequences from all organisms -- no matter how diverse -- show a pattern of inheritance.

                The vast majority of organisms (with exception *of sponges and possibly Kimberella) in the Ediacaran bear no resemblance to to those in the Cambrian. In other words the pre-cambrian 'animals' like dickinsonia, spriggina and charnia may be plants. They don't have head, gut, sensory organs, *eyes etc.
                The Cambrian is the first of mass the radiations following a mass extinction. So most of the Eidacaran organisms went extinct without descendents. The Cambrian organisms arose from different ancestors (soft-bodied). Several of these have been found:

                1. http://news.nationalgeographic.com/n...rustacean.html Crustacean pre-Cambrian but not hard-shelled.
                1a.http://cas.bellarmine.edu/tietjen/Ec..._evolution.htm Good summary of radiation from simpler to more complex<BR>
                2. Schopf, JW. Solution to Darwin's dilemma: Discovery of the missing Precambrian record of life. PNAS 97: 6947-6953, 2000. http://www.pnas.org/cgi/content/full/97/13/6947
                3. Ramskold, L and Hou, 1991 New early Cambrian Animal and Onychophoran
                Affinities of Enigmatic Metazoan. Nature, 351: 225-228
                4. RA Kerr, Pushing back the origin of animals, Science 279: 803-804, 6 Feb. 1998. The peer reviewed article is C-W Li, J-Y Chen, T-E Hua, Precambrian sponges with cellular structures. Science 279: 879-882. Got embryonic animal fossils that lived 40-50 million years before the Cambrian. Correlates with the molecular data and removes the Cambrian "explosion".
                5. Ramskold, L&nbsp; 1992&nbsp; The second leg row of Hallucigenia discovered. Lethaia, 25: 221-224
                6. S Jensen, JG Gehling, MI Droser, Ediacara-type fossils in Cambrian sediments. Nature 393: 567-569, June 11, 1998. Some ediacarans survived into the Cambrian period.
                7. HR Vandeberg, Fish tales: pushing back the dawn of the vertebrates. The Sciences 40: 9, Jan/Feb 2000. Describes new fossils from China of fish 530 Mya. First vertebrates. Nov. 4 1999 issue of Nature.
                10. RA Kerr, Tracks of billion year old animals? Science 282: 19-20, Oct. 2, 1998. Primary article is&nbsp; A Selachner, PK Bose, F Pfluger, Triploblastic animals more than 1 billion years ago: trace fossil evidence from India. Science 282: 80-83, Oct. 2, 1998. Shows tracks of worms 200-500 million years before Cambrian.
                If sound science appears to contradict the Bible, we may be sure that it is our interpretation of the Bible that is at fault." Christian Observer, 1832, pg. 437

                Comment


                • Originally posted by The Barbarian View Post
                  Denny wrote, earlier: [COLOR="DarkRed"]Here's just two of the things you 'forgot to include' Professor Stripe:"We have demonstrated that RNA editing is a major player in genetic information processing rather than an exception to the rule," said Dr. Eisenberg. "By showing that the squid's RNA-editing dramatically reshaped its entire proteome -- the entire set of proteins expressed by a genome, cell, tissue, or organism at a certain time -- we proved that an organism's self-editing of mRNA is a critical evolutionary and adaptive force.""The principle of adaptation -- the gradual modification of a species' structures and features -- is one of the pillars of evolution. While there exists ample evidence to support the slow, ongoing process that alters the genetic makeup of a species, scientists could only suspect that there were also organisms capable of transforming themselves ad hoc to adjust to changing conditions. (Emphasis added.)"So the scientists were expecting to find animals like this at some point, the study doesn't discredit evolution in the slightest [It actually credits this new discovery with proving mRNA editing as crucial to evolution in the bold font above], and the study says that both evolution and adaptation (STRIPE BELIEVES IN NEITHER) are supported by "ample evidence."Congratulations Stripe! You just disproved everything you have been saying on other related threads.[/COLOR]Did you think no one would notice what you deleted, Stipe?[/QUOTE][QUOTE=The Barbarian;4330594]The "biblical model" doesn't have much to do with the Bible.
                  Until you pick one among "six days" and "billions of years," everything you say can be justifiably ignored, as you haven't a rational leg to stand on when you cannot get the fundamentals right.

                  Originally posted by lucaspa View Post
                  And where is the Biblical justification for that?
                  Evidence, remember? That is what we look at. Organisms can be demonstrated to show adaptation. They cannot be shown to demonstrate evolutionary advance by means of random mutation and selection.

                  6days, "adaptation" is an ad hoc hypothesis to try to save creationism from falsification. Creationists could not deny all the observed examples of adaptation over generations. What they tried to do is say "adaptation within limits" of a "kind".
                  Fortunately, that is what we see.

                  That is a strawman. First you need to define "gradual". Then you need to define "adaptation".
                  Evolutionists hate dictionaries.

                  Originally posted by lucaspa View Post
                  What the article showed is that information is processed at mRNA level before it is translated to proteins. Not that big a deal. After all, information is introduced by the folding of the proteins after then come out of the ribosomes. Specific proteins (themselves coded by DNA) called chaperones do this. Also, proteins are glycosylated after synthesis, and in may cases (like proteoglycans), this is essential to their function. Again, the glycosylation is by other proteins, themselves coded by DNA. Some proteins, like HSP90, even determine which isomers of proteins will be transcribed to mRNA. HSP90 is reactive to the environment, but it itself is coded by DNA so it has evolved to do its job.
                  You're describing an overall effect in big words to avoid the challenge. How do random mutations and natural selection produce this process you just described?

                  We have a squid that uses its genetic information to recode its genetic information to suit an environment; completely undermining the theory of evolution.

                  If mutation and selection cannot account for the diversity of organisms, then there would be independent DNA sequences in different "kinds" of organisms.
                  There are.

                  OTOH, if mutation and selection do account for organisms, their DNA sequences will show patterns of inheritance (from those mutations and selection of an original in the common ancestor).
                  Or similar functions could have been designed similarly.

                  DNA sequences from all organisms -- no matter how diverse -- show a pattern of inheritance.
                  Nope. That's your evolutionism speaking. Religious adherence leads to blind faith.
                  Where is the evidence for a global flood?
                  E≈mc2
                  "the best maths don't need no stinkin' numbers"

                  "The waters under the 'expanse' were under the crust."
                  -Bob B.

                  Comment


                  • For anyone interested, you can get the full paper here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4384741/

                    Abstract:
                    RNA editing by adenosine deamination alters genetic information from the genomic blueprint. When it recodes mRNAs, it gives organisms the option to express diverse, functionally distinct, protein isoforms. All eumetazoans, from cnidarians to humans, express RNA editing enzymes. However, transcriptome-wide screens have only uncovered about 25 transcripts harboring conserved recoding RNA editing sites in mammals and several hundred recoding sites in Drosophila. These studies on few established models have led to the general assumption that recoding by RNA editing is extremely rare. Here we employ a novel bioinformatic approach with extensive validation to show that the squid Doryteuthis pealeii recodes proteins by RNA editing to an unprecedented extent. We identify 57,108 recoding sites in the nervous system, affecting the majority of the proteins studied. Recoding is tissue-dependent, and enriched in genes with neuronal and cytoskeletal functions, suggesting it plays an important role in brain physiology.

                    Some important points from the paper that refute the contention that this adaptation did not evolve. First is that it is rare. If God wanted organisms to adapt, why not put this mRNA editing scheme into ALL organisms?

                    From the Intro:
                    "DNA sequences were thought to exactly correspond with the sequence of amino acids in the resulting protein. However, it is now known that processes called RNA editing can change the nucleotide sequence of the mRNA molecules after they have been transcribed from the DNA. One such editing process, called A-to-I editing, alters the ‘A’ nucleotide so that the translation machinery reads it as a ‘G’ nucleotide instead. In some—but not all—cases, this event will change, or ‘recode’, the amino acid encoded by this stretch of mRNA, which may change how the protein behaves. This ability to create a range of proteins from a single DNA sequence could help organisms to evolve new traits."

                    Essentially, this is a another means of mutation. Point mutations do change an A to a G in the DNA; this method does so in the mRNA.

                    "Alon et al. have now developed a new approach that allows the recoding sites to be identified in organisms whose genomes have not been sequenced. Using this technique—which compares mRNA sequences with the DNA sequence they have been transcribed from—to examine the squid nervous system revealed over 57,000 recoding sites where an ‘A’ nucleotide had been modified to ‘G’ and thereby changed the coded amino acid. "

                    Basically, the squid uses this method of mutation to generate different variations of about 60% of the squid's proteins.

                    "Recently, it was suggested that RNA editing is generally not advantageous in humans (Xu and Zhang, 2014), as nonsynonymous events are less frequent than expected by chance (Xu and Zhang, 2014). Strikingly, for sites with high editing levels in squid, the opposite is true (Figure 4B and Figure 4—figure supplement 2A). Recoding events favor creation of glycine and arginine, mainly at the expense of lysine (Figure 4—figure supplement 2B–D). Moreover, highly edited sites within conserved domains tend to recode to amino acids that occur frequently in other species at the same position (Figure 4—figure supplement 3), suggesting selection towards functional substitutions and against deleterious ones."

                    Oops. Not design, but natural selection.

                    "An equally intriguing question is why squid edit to this extent? The process clearly creates tremendous protein diversity, and this may in part explain the behavioral sophistication of these complex invertebrates. A recent study showed that editing can be used for temperature adaptation in octopus (Garrett and Rosenthal, 2012b) and this makes sense based on the codon changes that it catalyzes (Garrett and Rosenthal, 2012a) (Figure 4—figure supplement 2C–D). In Drosophila, editing can respond to acute temperature changes (Savva et al., 2012). The large number of sites in squid suggests that editing is well positioned to respond to environmental variation. Most model organisms studied so far are mammals which are homeotherms. Future studies of more diverse species are needed to reveal the extent to which cold-blooded organisms might utilize extensive editing to respond to temperature changes and other environmental variables."

                    So, as usual the "news article" has overstated the claims. Squids are cold-blooded, but they face a wide variety of water temperatures. Enzymes behave differently at different temperatures. In order to adapt to living in so many different water temperatures, squids have evolved (over millions of years by gradual evolution) this particular system (not extensively used by other species) to generate lots of variations of key proteins. Why? So that some of them will function as the squid moves from cold to warm to cold water again. The proteins have to be in existence all the time, because there is no time to transcribe a different protein in the seconds that the squid moves between water temps. This process has evolved -- by gradual evolution -- in both the ADAR (adenosine deaminase that acts on RNA) enzyme and in the DNA sequence in proteins to provide sites for the ADAR.

                    Nothing in the paper to challenge evolution, or even the Modern Synthesis. The challenge comes from a distorted news article and the imagination and desperation of creationists.

                    God created by evolution. Get over it.
                    If sound science appears to contradict the Bible, we may be sure that it is our interpretation of the Bible that is at fault." Christian Observer, 1832, pg. 437

                    Comment


                    • Originally posted by Stripe View Post
                      Religious adherence leads to blind faith.
                      Is there any other kind? (Hebrews 11:1; Romans 8:24)

                      Comment


                      • Originally posted by lucaspa View Post
                        God created by evolution. Get over it.
                        Nope. That's the demands of your evolutionism. When you're prepared to drop the assumption of your religion and address the challenge, let us know.

                        Originally posted by User Name View Post
                        Is there any other kind?
                        Yes. Justification.
                        Where is the evidence for a global flood?
                        E≈mc2
                        "the best maths don't need no stinkin' numbers"

                        "The waters under the 'expanse' were under the crust."
                        -Bob B.

                        Comment


                        • Originally posted by Stripe View Post
                          Until you pick one among "six days" and "billions of years," everything you say can be justifiably ignored, as you haven't a rational leg to stand on when you cannot get the fundamentals right.


                          The irony is too much sometimes. Stripe giving lessons on "rational legs" is like a wolf giving lesson on having a vegan diet. First, he doesn't understand the difference. And second he does not have the self control to not "wolf down" some rotted meat should the opportunity present itself.

                          The fundamentals of epistemology do not start with Stripe's proclaimed split of either 6 days or billions of years. I think that YEC's have gotten so use to trying to rewrite science with their nonsensical ideas, it becomes second nature to try and rewrite just about every idea they come in contact with.
                          Militant Moderate

                          Comment


                          • Originally posted by Stripe View Post
                            Yes. Justification.
                            Justification negates faith?

                            Comment


                            • Originally posted by Stripe View Post
                              Nope. That's the demands of your evolutionism. When you're prepared to drop the assumption of your religion and address the challenge, let us know.



                              Yes. Justification.
                              Taking two "evilustionists" on in one post. You are bad (I mean that in a good way) Stripe. I bet your little cheering section here is real proud of your ability to churn up nonsense.
                              Militant Moderate

                              Comment


                              • Originally posted by User Name View Post
                                Justification negates faith?
                                Where is the evidence for a global flood?
                                E≈mc2
                                "the best maths don't need no stinkin' numbers"

                                "The waters under the 'expanse' were under the crust."
                                -Bob B.

                                Comment

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