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A liberating voice on the feathered dragons

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Evolution: Education and Outreach is usually a disappointment. The journal could do with more philosophically savvy writers and more critical reviewers. The various contributions provide very little evidence that they understand Kuhn’s thesis about the way science develops. Most of the authors are working in a silo and fail to understand anyone who operates outside their tightly defined paradigm. A notable exception was Daniel R. Brooks (2011) who wrote on “The Extended Synthesis: Something Old, Something New” (blogged here). Another is the theme of this blog: a review of Alan Feduccia’s “Riddle of the Feathered Dragons” by Egbert Giles Leigh Jr. What caught my eye was the acknowledgement that Feduccia provides a “powerful criticism of prevailing views of bird evolution”. Leigh explains that he is relatively new to this theme, and he appears shocked to find out what an intense battlefield he was entering.

“I was blissfully unaware of the raging dispute over just what group of reptiles gave rise to birds. The introduction, which opens with bitter comments on uncritical media hype about dinosaur ‘discoveries’, and the first chapter, subtitled ‘Blame to Go Around’, cured me rather brutally of that ignorance.” (p.1)

Leigh summarises the arguments of John Ostrom, who championed the thesis that birds evolved from theropod dinosaurs. He knew that dinosaurs like Deinonychus had many similarities with Archaeopteryx, and he promoted the idea that flight evolved ground up. The ancestors of birds were considered to be runners, flapping their forelimbs to catch insects, thereby evolving the functionality for flapping flight. Leigh reports Feduccia’s objections to Ostrom, obviously impressed by his arguments, and noting that “More recently, the tide of evidence has turned strongly against Ostrom’s case.” Part of this evidence relates to protofeathers, and Leigh is positive about the case for them being collagen fibres. (For further on this, go here and here.)

“The discovery that the ‘protofeathers’ of the bipedal, cursorial theropod Sinosauropteryx were collagen fibers representing various stages of skin decay (Lingham-Soliar et al. 2007) undermined the argument that feathers evolved for purposes other than flight. If Anchiornis and Archaeopteryx were ancestral birds, it would appear that that feathers, which Feduccia shows to be complex, intricate structures well adapted for flight, evolved for that purpose. Feathered wings did not first evolve to be clapped together to catch insects, as Ostrom (1974, 1979) had proposed.” (p.2)

The reason why this is important relates to the major point being made by Leigh: “The argument between Feduccia and Ostrom was later engulfed by a methodological one.” This methodological issue concerns cladism. Rarely does one read words like this:

“This method seemed to lend an objective rigor to inferring phylogenies from phenotypic data. Many practitioners of this method proclaim that birds derive from theropod dinosaurs.” (p.2)

What follows is one of the best concise critiques of cladism that I have read. It deserves to be quoted in full, but this seems unwise – especially as the review is Open Access. The issue of protofeathers is located at the beginning of the critique. If they are interpreted as primitive feathers, they constrain the cladistic analysis towards the theropod-bird evolutionary pathway. If however they represent collagen fibres released during skin decay, the outcome is quite different. Leigh sees this as an example of scientists craving for an objectivity that brings authority, latching on to a method that seems to offer this, and losing sight of other data that disturbs their conclusions.

“More generally, the search for the one objective scientific method, where subjective judgments play no role, is a recipe for ignoring what is crucial. So it was for the psychologists who saw stimulus-response analyses as the way to make animal behavior an objective science by avoiding the subjective world of consciousness. As Changeux (1985, p. 97) remarked, ‘Concerned with eliminating subjectivity from scientific observation, behaviorism restricted itself to considering the relationship between variations in the environment (the stimulus) and the motor response that was provoked’. This approach does not let us see that animals have intentions and project their hypotheses onto the external world (Changeux and Ricoeur 2000, p. 42). Is this also true of those cladists who see a particular algorithm for inferring phylogenies from phenotypic data as the one way to practice objective taxonomy? Such methods demand that their practitioners ignore those kinds of data that their methods cannot handle. Indeed, as in the case of scientific Marxism, supposed recipes for objectivity can become dogmas defended with religious zeal (Polanyi 1962, pp. 227-228). Feduccia (p. 2) cites instances of this process among some cladists. This process can discourage interesting science, as did the Roman inquisition of the 17th century (Changeux and Ricoeur 2000, p. 35). Feyerabend’s (1975) Against Method is a salutary warning against seeking one scientific method, apt for solving all problems.” (p.3)

In his concluding words, Leigh points to the BAD advocates (Birds Are Dinosaurs) as “intellectual prisoners of their cladistic methodology”. Although he represents the minority BAND (Birds Are Not Dinosaurs), and although the controversy is draining, Feduccia is presented as the champion of authentic science.

“[H]is book is eloquent testimony to the role of connoisseurship in effective science. For all its bitterness, Feduccia’s is a liberating voice, a reminder that methodology should be our servant, not our unquestioned master.” (p.3)

It’s a great review and it deserves to be widely read. This is not just a controversy over dino-fuzz – it has the potential to stimulate thinking about the way science is practised.

Alan Feduccia’s Riddle of the Feathered Dragons: what reptiles gave rise to birds?
Egbert Giles Leigh Jr
Evolution: Education and Outreach, March 2014, 7:9, (3 pages)

This book’s author is at home in the paleontology, anatomy, physiology, and behavior of birds. Who could be more qualified to write on their origin and evolution? This book is unusually, indeed wonderfully, well and clearly illustrated: its producers cannot be praised too highly. It is well worth the while of anyone interested in bird evolution to read it. [snip]

Comments
(I'm almost beginning to suspect the anti-evolutionists "skepticism" is very selectively applied...)wd400
June 6, 2014
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If this sequence was in the tiny minority that are exonic then you'd have a broken gene. If Tomkins wanted to say small nucleotide differences can make large practical difference then he could have. But that's not what he's saying. He's saying those two sequences are 60% similar. I invite anyone who wants to defend that claim to do so....wd400
June 6, 2014
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wd400:
ATAGTCGATCGATCGATCGTACGAGGGGGGGTACGTACGTAGCATCGTAGTCAGACTG ATAGTCGATCGATCGATCGTACGAGGGGGGGTACGACGTAGCATCGTAGTCAGACTG
I think 'willh' was trying to ask this question, so I'll just go ahead and ask it: If the sequence you give is off only by 2%, does this mean that it is off by 2% when it comes to 'translation'? IOW, what would the a.a. sequence look like vis-a-vis the nucleotide sequence? Why would mRNA, or tRNA, go along this sequence and then say: "Well, obviously these two sequences are meant to be the same, so I'll just delete the one nucleotide, and then code for the rest." But, of course, there is nothing to compare to, since the sequence is either the one, or the other. Hence, I don't see how the translational apparatus of the cell is going to do anything other than to translate the latter part of the sequence in terms of very different a.a.s.PaV
June 6, 2014
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Yes, that is a good video. I hope Sternberg publishes a paper on his work soon. Better yet, I hope that Sternberg and Tomkins collaborate on a paper. Now that would be a paper worth reading! :)bornagain77
June 5, 2014
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bonagain77, Thanks for posting the Bohlin video---provocative and fascinating! Seems like there's a parallel between evolutionists' wanting to obscure the significance of junk . . . er, I mean non-coding DNA, and the Wizard of Oz not wanting Dorothy to look behind the curtain. -QQuerius
June 5, 2014
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wd400, so if you threw out everything that did not match as atheists do with their biased analysis of human chimp comparison you would get 70%??? Funny that is the figure that Tomkins reached. :) You see wd400, (although you think you already know everything and nobody understands evolution save you and a few other elites) it might interest you to know that if you threw out everything that did not match, as atheists do in their biased comparisons of chimps and humans (even neglecting ORFans in many studies), you would approach 100% similarity for kangaroos and humans as atheists did. But if you compare genomes as you say 'normally' then you will get a gene count number that is rather stable across genomes: Evolution by Splicing – Comparing gene transcripts from different species reveals surprising splicing diversity. – Ruth Williams – December 20, 2012 Excerpt: A major question in vertebrate evolutionary biology is “how do physical and behavioral differences arise if we have a very similar set of genes to that of the mouse, chicken, or frog?”,,, A commonly discussed mechanism was variable levels of gene expression, but both Blencowe and Chris Burge,,, found that gene expression is relatively conserved among species. On the other hand, the papers show that most alternative splicing events differ widely between even closely related species. “The alternative splicing patterns are very different even between humans and chimpanzees,” said Blencowe.,,, http://www.the-scientist.com/?articles.view%2FarticleNo%2F33782%2Ftitle%2FEvolution-by-Splicing%2F "Where (chimps and humans) really differ, and they differ by orders of magnitude, is in the genomic architecture outside the protein coding regions. They are vastly, vastly, different.,, The structural, the organization, the regulatory sequences, the hierarchy for how things are organized and used are vastly different between a chimpanzee and a human being in their genomes." Raymond Bohlin (per Richard Sternberg) - 9:29 minute mark of video http://www.metacafe.com/watch/8593991/ Moreover, where the difference is greatest is where the genome is found to be least likely to tolerate changes, thus undermining Darwinian claims for plasticity: A Listener's Guide to the Meyer-Marshall Debate: Focus on the Origin of Information Question -Casey Luskin - December 4, 2013 Excerpt: "There is always an observable consequence if a dGRN (developmental gene regulatory network) subcircuit is interrupted. Since these consequences are always catastrophically bad, flexibility is minimal, and since the subcircuits are all interconnected, the whole network partakes of the quality that there is only one way for things to work. And indeed the embryos of each species develop in only one way." - Eric Davidson http://www.evolutionnews.org/2013/12/a_listeners_gui079811.html Darwin or Design? - Paul Nelson at Saddleback Church - Nov. 2012 - ontogenetic depth (excellent update) - video Text from one of the Saddleback slides: 1. Animal body plans are built in each generation by a stepwise process, from the fertilized egg to the many cells of the adult. The earliest stages in this process determine what follows. 2. Thus, to change -- that is, to evolve -- any body plan, mutations expressed early in development must occur, be viable, and be stably transmitted to offspring. 3. But such early-acting mutations of global effect are those least likely to be tolerated by the embryo. Losses of structures are the only exception to this otherwise universal generalization about animal development and evolution. Many species will tolerate phenotypic losses if their local (environmental) circumstances are favorable. Hence island or cave fauna often lose (for instance) wings or eyes. http://www.saddleback.com/mc/m/7ece8/bornagain77
June 5, 2014
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No questions are forebidden - you've just shown yourself to not be worth my time. FWIW, I gather human and marsupial genes show about 70% identity using normal genetic measures. How knows what you'd get if your threw Tomkins method at it.wd400
June 4, 2014
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So the people who did the analysis state ",,,”We thought they’d be completely scrambled, but they’re not." and yet wd400 states it is not really that surprising at all. They are merely 'conserved'. i.e. WA LA wave the magic Darwin wand and all problems disappear.,,, And remember don't ever, ever, ask to peek up his sleeve for actual empirical evidence! :) Just sit back and enjoy the show! For instance, questions like this are forbidden: But wd400, if you threw out everything that did not match, how close do you think kangaroos would be to humans?bornagain77
June 4, 2014
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According to some, this is even Greater Proof of Convergent Evolution! Nope. There's no suggestion of convergent evolution between human and kanagaroo genomes. This result is about shared genes, and that the order in which some those shared genes line up on chromosomes is conserved (the exact opposite of convergence actually). Since you've tried to make something out of Tomkins results, do you agree with him that the sequences I posted about are ~60 similar? If you don't, what do you make of his human chimp studies now?wd400
June 4, 2014
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OT: podcast - "Jonathan Wells: Is There Biological Information Outside of the DNA?, pt. 2" http://intelligentdesign.podomatic.com/entry/2014-06-04T16_31_53-07_00 Stephen Meyer - Advancing the Scientific Debate - video https://www.youtube.com/watch?v=kNCpBYus7dsbornagain77
June 4, 2014
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bornagain77 excerpted,
There is great chunks of the human genome which is sitting right there in the kangaroo genome
According to some, this is even Greater Proof of Convergent Evolution! To me it indicates something really interesting is going on. -QQuerius
June 4, 2014
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"That doesn’t seem like a reasonable way of comparing these sequences to me" Thus once again I ask,, wd400, if you threw out everything that did not match, how close do you think kangaroos would be to humans? Kangaroo genes close to humans Excerpt: Australia’s kangaroos are genetically similar to humans,,, “There are a few differences, we have a few more of this, a few less of that, but they are the same genes and a lot of them are in the same order,” ,,,”We thought they’d be completely scrambled, but they’re not. There is great chunks of the human genome which is sitting right there in the kangaroo genome,”bornagain77
June 3, 2014
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Hmm, the WordPress html parser doesn't like tags it seems. The middle alignment should be: ATAGTCGATCGATCGATCGTACGAGGGGGGGTACGTACGTAGCATCGTAGTCAGACTG ATAGTCGATCGATCGATCGTACGAGGGGGGGTAC-GACGTAGCATCGTAGTCAGACTG wd400
June 3, 2014
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Willh, It's not really expressoin (in the biological sense) or function, but a purely methodological question. Given those examplar sequences ATAGTCGATCGATCGATCGTACGAGGGGGGGTACGTACGTAGCATCGTAGTCAGACTG ATAGTCGATCGATCGATCGTACGAGGGGGGGTACGACGTAGCATCGTAGTCAGACTG it seems to be the sensible alignment is ATAGTCGATCGATCGATCGTACGAGGGGGGGTACGTACGTAGCATCGTAGTCAGACTG ATAGTCGATCGATCGATCGTACGAGGGGGGGTAC-GACGTAGCATCGTAGTCAGACTG where ~98 of bases are shared. Tomkins, as far as I can tell, explicitly prevents gaps so his method would say this is the best alignment possible ATAGTCGATCGATCGATCGTACGAGGGGGGGTAC ATAGTCGATCGATCGATCGTACGAGGGGGGGTAC The way he counts similarity he'd say only 35 of the 58 bases align so these sequences are about ~60% percent similar. That doesn't seem like a reasonable way of comparing these sequences to mewd400
June 3, 2014
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wd400, Ok now I see a bit better what your getting at. My change in function question, though I'm sure a bit naive, was only to make some sense of any 'real' (even though your example is a hypothetical gene) effect causing the 98% difference to drop to a 60ish%. But now it's one of a view of expression and not function perhaps? Begging pardons all round. I think though that an argument as to why the differences, beyond what differences should be included, exists ... but that is perhaps another topic or the next one maybe?willh
June 3, 2014
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willh, This isn't a real gene - it's just illustrative of what Tomkins method does. Those two sequences differ by one indel (there's one base present in the first that's not present in the second) so it seems to me like they are 57/58 ~ 98% identical. The way Tomkins runs his analyses the sequences would score ~60% as he counts only the largest alignable and does not allow gaps in the alignment. A small nucleotide difference can certainly make a large practical difference (though I should point out almost none of the genome codes for proteins), but that's not the point Tomkins makes. It seems a very stange way to compare genomes to me....wd400
June 3, 2014
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wd400, if you threw out everything that did not match, how close do you think kangaroos would be to humans? Kangaroo genes close to humans Excerpt: Australia's kangaroos are genetically similar to humans,,, "There are a few differences, we have a few more of this, a few less of that, but they are the same genes and a lot of them are in the same order," ,,,"We thought they'd be completely scrambled, but they're not. There is great chunks of the human genome which is sitting right there in the kangaroo genome," http://www.reuters.com/article/science%20News/idUSTRE4AH1P020081118bornagain77
June 3, 2014
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Professor Jerry Fodor confessed, ‘I don’t think anybody knows how evolution works.’ http://creation.com/creation-religious-educationbornagain77
June 3, 2014
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Dang your right wd400, it turns out that even Harvard trained biologists 'Don't Really Get Evolution" A New Hire at the National Center for Science Education Admits "Many of Us Don't Really Get Evolution" - Donald McLaughlin June 3, 2014 http://www.evolutionnews.org/2014/06/a_new_hire_at_t086351.htmlbornagain77
June 3, 2014
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wd400 wrote @ 110: ATAGTCGATCGATCGATCGTACGAGGGGGGGTACGTACGTAGCATCGTAGTCAGACTG ATAGTCGATCGATCGATCGTACGAGGGGGGGTACGACGTAGCATCGTAGTCAGACTG Ok I'll bight. What is the effect of the possible extra 'T' nucleotide in the first string? Does it cause no change to the reading of the base triplets (I count 19 base triplets in the lower sequence and 19 base triplets +1 single nucleotide base in the upper sequence ... err I think), is it an 'indel' and will be ignored, or are all the following base triplets now totally different due to a 'shifting' by one location in the code read?willh
June 3, 2014
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Hey PaV, Actually that quote is from his correspondence. http://www.darwinproject.ac.uk/letter/entry-3154Mung
June 3, 2014
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Mung: Quoting Darwin from the Origins:
“The point which you raise on intelligent Design has perplexed me beyond measure… I am in a complete jumble… One cannot look at this Universe…without believing that all has been intelligently designed; yet when I look to each individual organism, I can see no evidence of this…”
I never noticed this before, but Darwin's logic here seems to almost perfectly parallel Hume's view on 'causality.' When you look at things real close, Hume would say, you can't "see" causality, you only "see" one thing happening after another thing. Yes, the errors of "empiricism"!PaV
June 3, 2014
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The BLASTN analyses done in this paper were performed after stripping all N’s from the data set and sequence slicing the large contiguous sequence into optimized slice sizes – all done on a local server using optimized algorithm parameters. My data not only takes into account gaps, but sequences present in human and absent in chimp, and vice versa. Doing an amateur armchair analysis on the BLAST web server with default parameters never designed for a one-on-one large scale genomic regional comparison as noted in the comment above by aceofspades25 is bogus. Of course, if the paper was actually read in it’s entirety in regards to the above comments this would have been obvious. Also, as noted in several evolutionary papers, which I cited in my paper, the large scale comparison and major differences in structural variability surrounding the GULO regions between humans and great apes in the intronic areas has been noted before. Interesting that the misleading post by aceofspades25 did not make note of that. My paper was in fact accurate in all respects and true to previous findings published by evolutionist themselves. My work just hashed out and exposed what was already known, but never previously elaborated upon because it shows just another aspect of what a complete fraud the human evolution paradigm truly is. https://uncommondescent.com/human-evolution/evolutionary-convergence-saves-creationist-hypothesis-over-gulo/#comment-500813bornagain77
June 3, 2014
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BA77 I would be interested in reading Tomkins reply to AoS criticisms. Can you point to where he responded to them on UD? I was unaware that he did so.JLAfan2001
June 3, 2014
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wd400, since you are personally having trouble with Dr. Tomkins methodology, and you are trained in the field, why don't you write him and ask him? He was kind enough to visit this blog once to set Ace's criticisms straight,,, and I'm sure if you write him a nice e-mail, you two can have a amicable discussion as to where you two disagree. Who knows perhaps you can make him finally see that he 'just doesn't understand evolution'. :)bornagain77
June 3, 2014
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So, reading closely over Tomkins papers it really seems like he would count and alignment between these two sequences: ATAGTCGATCGATCGATCGTACGAGGGGGGGTACGTACGTAGCATCGTAGTCAGACTG ATAGTCGATCGATCGATCGTACGAGGGGGGGTACGACGTAGCATCGTAGTCAGACTG as being ~60% similar, as he doesn't allow gaps in alignment and counts one alignment per query sequence:
BLASTN algorithm parameters for the main study were as follows: -word_size 11, -evalue 10, -max_target_seqs 1, -dust no, -soft_masking false, -ungapped.
Does anyone thing those two sequences are 60% similar? Does anyone want to back down from their support of the 70% claim?wd400
June 3, 2014
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This is very interesting (at least for me) as to undermining neo-Darwinism:
Peer-Reviewed Paper: Development Needs Ontogenetic Information that Cannot Arise from Neo-Darwinian Mechanisms - Casey Luskin - June 2, 2014 Excerpt: ,,,"the vast majority of proteins in eukaryotes are not completely specified by DNA sequences.",,, Jonathan Wells http://www.evolutionnews.org/2014/06/peer-reviewed_p_2086201.html
I went to Dr. Wells's paper and found on page 11:
Membrane Patterns Carry Ontogenetic Information That Is Specified Independently of DNA - 2014 Jonathan Wells Excerpt Page 11: Most proteins are not completely specified by DNA sequences: The central dogma (which here includes Crick’s sequence hypothesis) claims that (1) DNA specifies RNA and (2) RNA specifies protein. Yet this claim fails at both steps, because most RNAs are not uniquely specified by DNA sequences, and many proteins are not uniquely specified by RNAs—either in their amino acid sequences or in their final folded forms. After transcription, RNAs from many eukaryotic genes undergo alternative splicing. Recent studies estimate that transcripts from approximately 95% of multi-exon human genes are spliced in more than one way [289?291]. By intervening between transcription and translation, alternative splicing generates RNAs with sequences that differ from DNA sequences [292]. The differences are functionally significant.,,, Page 12 In addition to alternative splicing, many metazoan transcripts undergo RNA editing, which can (a) modify cytidine to uridine; (b) modify adenosine to inosine; or (c) insert additional nucleotides. Several recent analyses have demonstrated extensive RNA editing in the human transcriptome [303?305]. The editing of an mRNA often alters the amino acid sequence of the encoded protein so that it differs from the sequence predicted by the DNA [306,307]. References: 289. Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, et al. (2008) Alternative isoform regulation in human tissue transcriptomes. Nature 456:470-476. doi: 10.1038/nature07509 290. Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 40:1413-1415. doi: 10.1038/ng.259 291. Barash Y, Calarco JA, Gao W, Pan Q, Wang X, et al. (2010) Deciphering the splicing code. Nature 465:53-59. doi: 10.1038/nature09000 292. Kornblihtt AR, Schor IE, Alló M, Dujardin G, Petrillo E, et al. (2013) Alternative splicing: A pivotal step between eukaryotic transcription and translation. Nat Rev Mol Cell Biol 14:153-165. doi: 10.1038/nrm3525 303. Peng Z, Cheng Y, Tan BC, Kang L, Tian Z, et al. (2012) Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome. Nat Biotechnol 30:253-260. doi: 10.1038/nbt.2122 304. Bahn JH, Lee JH, Li G, Greer C, Peng G, et al. (2012) Accurate identification of A-to-I RNA editing in human by transcriptome sequencing. Genome Res 22:142-150. doi: 10.1101/gr.124107.111 305. Sakurai M, Ueda H, Yano T, Okada S, Terajima H (2014) A biochemical landscape of A-to-I RNA editing in the human brain transcriptome. Genome Res (January 9, 2014). doi: 10.1101/gr.162537.113 306. Brennicke A, Marchfelder A, Binder S (1999) RNA editing. FEMS Microbiol Rev 23:297-316. doi: 10.1111/j.1574-6976.1999.tb00401.x 307. Eisenberg E, Li JB, Levanon EY (2010) Sequence based identification of RNA editing sites. RNA Biol 7:248-252. doi: 10.4161/rna.7.2.11565 http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2014.2/BIO-C.2014.2
bornagain77
June 3, 2014
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podcast - "Jonathan Wells: Is There Biological Information Outside of the DNA?" http://intelligentdesign.podomatic.com/entry/2014-06-02T18_00_49-07_00 i.e. wd400's primary assumption of neo-Darwinism is false!bornagain77
June 3, 2014
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As to Darwinists 'fessing up' to the 1% myth: The Chimp-Human 1% Difference: A Useful Lie - 06/29/2007 Excerpt: “For many, many years, the 1% difference served us well because it was underappreciated how similar we were,” says Pascal Gagneux, a zoologist at UC San Diego. “Now it’s totally clear that it’s more a hindrance for understanding than a help.”,,, This is a very disturbing article. We have basically caught the Darwinists in a bald lie that has hoodwinked the world for over 30 years. Gagneux says, “For many, many years, the 1% difference served us well” – stop right there! Who is “us”? Was it the millions of school children and laymen who were lied to? Was it the majority of people who believe God created mankind, suffering under an onslaught of lies told in the name of science? No! “Us” refers to the members of the Darwin Party,,, http://creationsafaris.com/crev200706.htm#20070629a Disturbing indeed. He is totally oblivious to his own 'confirmation bias' revealed in his statement. Only in Darwinian 'science' is such bias/blindness tolerated as if it is normal for science to operate in such a biased fashion. Supplemental notes: In “Science,” 1975, M-C King and A.C. Wilson were the first to publish a paper estimating the degree of similarity between the human and the chimpanzee genome. This documented the degree of genetic similarity between the two! The study, using a limited data set, found that we were far more similar than was thought possible at the time. Hence, we must be one with apes mustn't we? But…in the second section of their paper King and Wilson honestly describe the deficiencies of such reasoning: “The molecular similarity between chimpanzees and humans is extraordinary because they differ far more than sibling species in anatomy and way of life. Although humans and chimpanzees are rather similar in the structure of the thorax and arms, they differ substantially not only in brain size but also in the anatomy of the pelvis, foot, and jaws, as well as in relative lengths of limbs and digits (38). Humans and chimpanzees also differ significantly in many other anatomical respects, to the extent that nearly every bone in the body of a chimpanzee is readily distinguishable in shape or size from its human counterpart (38). Associated with these anatomical differences there are, of course, major differences in posture (see cover picture), mode of locomotion, methods of procuring food, and means of communication. Because of these major differences in anatomy and way of life, biologists place the two species not just in separate genera but in separate families (39). So it appears that molecular and organismal methods of evaluating the chimpanzee human difference yield quite different conclusions (40).” King and Wilson went on to suggest that the morphological and behavioral between humans and apes,, must be due to variations in their genomic regulatory systems. David Berlinski - The Devil's Delusion - Page 162&163 Evolution at Two Levels in Humans and Chimpanzees Mary-Claire King; A. C. Wilson - 1975 http://academic.reed.edu/biology/professors/srenn/pages/teaching/BIO431S05_2008/431S05_readings/431s05_examples/king_wilson_1975(classic).pdf The Red Ape - Cornelius Hunter - August 2009 Excerpt: "There remains, however, a paradoxical problem lurking within the wealth of DNA data: our morphology and physiology have very little, if anything, uniquely in common with chimpanzees to corroborate a unique common ancestor. Most of the characters we do share with chimpanzees also occur in other primates, and in sexual biology and reproduction we could hardly be more different. It would be an understatement to think of this as an evolutionary puzzle." http://darwins-god.blogspot.com/2009/08/red-ape.html Mona Lisa smile: The morphological enigma of human and great ape evolution - 2006 Excerpt: The quality and scope of published documentation and verification of morphological features suggests there is very little in morphology to support a unique common ancestor for humans and chimpanzees.,,, http://onlinelibrary.wiley.com/doi/10.1002/ar.b.20107/abstract In fact so great are the anatomical differences between humans and chimps that a Darwinist actually proposed that a chimp and pig mated with each other and that is what ultimately gave rise to humans: A chimp-pig hybrid origin for humans? - July 3, 2013 Excerpt: Dr. Eugene McCarthy,, has amassed an impressive body of evidence suggesting that human origins can be best explained by hybridization between pigs and chimpanzees. Extraordinary theories require extraordinary evidence and McCarthy does not disappoint. Rather than relying on genetic sequence comparisons, he instead offers extensive anatomical comparisons, each of which may be individually assailable, but startling when taken together.,,, The list of anatomical specializations we may have gained from porcine philandering is too long to detail here. Suffice it to say, similarities in the face, skin and organ microstructure alone is hard to explain away. A short list of differential features, for example, would include, multipyramidal kidney structure, presence of dermal melanocytes, melanoma, absence of a primate baculum (penis bone), surface lipid and carbohydrate composition of cell membranes, vocal cord structure, laryngeal sacs, diverticuli of the fetal stomach, intestinal "valves of Kerkring," heart chamber symmetry, skin and cranial vasculature and method of cooling, and tooth structure. Other features occasionally seen in humans, like bicornuate uteruses and supernumerary nipples, would also be difficult to incorporate into a purely primate tree. http://phys.org/news/2013-07-chimp-pig-hybrid-humans.html Moreover, Physorg published a subsequent article showing that the pig-chimp hybrid theory for human origins is much harder to shoot down than Darwinists had first supposed it would be: Human hybrids: a closer look at the theory and evidence - July 25, 2013 Excerpt: There was considerable fallout, both positive and negative, from our first story covering the radical pig-chimp hybrid theory put forth by Dr. Eugene McCarthy,,,By and large, those coming out against the theory had surprisingly little science to offer in their sometimes personal attacks against McCarthy. ,,,Under the alternative hypothesis (humans are not pig-chimp hybrids), the assumption is that humans and chimpanzees are equally distant from pigs. You would therefore expect chimp traits not seen in humans to be present in pigs at about the same rate as are human traits not found in chimps. However, when he searched the literature for traits that distinguish humans and chimps, and compiled a lengthy list of such traits, he found that it was always humans who were similar to pigs with respect to these traits. This finding is inconsistent with the possibility that humans are not pig-chimp hybrids, that is, it rejects that hypothesis.,,, http://phys.org/news/2013-07-human-hybrids-closer-theory-evidence.html The obvious question for me is, of course, since Darwinists are having such a hard time proving that we did not come from pig-chimp hybrids, what makes Darwinists so sure that we evolved from apes or anything else in the first place? Any reasonable person would realize that if such a dubious theory as the pig-chimp hybrid theory can cause such havoc, for what was suppose to be such well established science, then perhaps the Darwinian theory for human origins is not nearly as strong as Darwinists have dogmatically held it to be in the first place. Some might even hold that such 'flimsiness' would clearly indicate the original theory was rubbish as to being hard science.bornagain77
June 3, 2014
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Interesting link Querius,,, Geneticist Jeff Tomkins vs. Evolutionary Biologist who got laughed off stage - August 12, 2013 Excerpt: Tomkins described the origin of the fallacious comparison as a myth that got started in reassociation kinetic methods of comparison in the mid-1970?s prior to the advent of modern sequencing techniques (like Illumina and Solexa). Reassociation kinetics was a technique where fragments of chimp and human DNA were mixed in the same chemical soup, and the DNAs that were reasonably similar would pair up, hence we got a biased sampling! If we take genes that are found in both humans and chimps and disregard the indels, we get the 98% figure. When indels are considered, the similarity drops to 80-85%! When including other sequences, the similarity drops even further, down to 70%. But that 70% figure itself, imho, is too generous. I don’t think Tomkins used ORFans or pseudo genes or many other intergenic sequences, and he explicitly avoided the complication of Synteny.... Tomkins pointed also to reports where lab workers may have contaminated the sequencing labs for Chimps with their own human DNA and thus biasing the figures! Hence re-sequencing has been done, and there is more sequencing pending to clean up these errors. He joked about the coughing and sneezing that may have gone on to cause contamination. Further he pointed out that it seemed politically incorrect to dispute the 98% figure promoted by the reassociation kinetics work because it accorded with the false evolutionary narrative. He said, the industry is finally having to “fess up”, that some of their conclusions are “bogus”. Tomkins has been reviewer on peer reviewed papers on genetics, he ran a genome lab at Clemson, and said if he had been the reviewer of some of the evolutionary papers he would have rejected them for publication because of the lack of clarity in their methodology, particularly in the material and methods sections of the paper. During the answer and question session, a ranting raving evolutionary biologists gets up and whines and says something to the effect, “you’re using such inflammatory language … ‘sneeze and cough and ‘fess up’ and bogus’”. The evolutionary biologist then said, “as I said, what I have problems with is inflammatory your language, I don’t want to get into the technical details.” When he said that, he got laughed off stage. It was obvious Tomkins made an unassailable case and the evolutionary biologist didn’t want to be engage Tomkins technical assertions. Instead the evolutionary biologist grasped at irrelevant straws like Tomkins use of the words “sneeze” and “cough”. Pathetic! https://uncommondescent.com/genetics/icc-2013-geneticist-jeff-tomkins-vs-evolutionary-biologist-who-got-laughed-off-stage/ So apparently wd400 thinks that for Dr. Tomkins to deal with indels 'properly' would be to delete them from the comparison so as to get a more 'proper' conclusion, but does wd400 have reason, besides wanting his conclusion to be true, for excluding the sequences from comparison? I certainly think wd400 does not have that warrant: Of related note to Tomkins 'methodology': When evolutionists talk about creatures sharing the same genes, they are typically referring to very small segments of DNA in the genome. And in most cases, they are only referring to the small pieces of protein-encoding genes called exons—not the whole segment of DNA that is actually responsible for producing the information to make the correct version of the protein at the right time and in the correct amount. http://www.icr.org/article/8129/ So if you assume evolution and exclude all other sequences in the gene that do not match, you get an evolutionary conclusion (no surprise there), but if you look at the 'whole segment of DNA that is actually responsible for producing the information to make the correct version of the protein at the right time and in the correct amount', you get a non-Darwinian conclusion. ,,,, It is easy to see why wd400 says Tomkins did not deal with indels 'properly'. Tomkins refuses to let evolutionary presuppositions dictate what he considers a 'gene', and to discard indels, but let what actually makes a protein dictate how he looks at the data.bornagain77
June 3, 2014
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