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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
Sorry, here is the Meyer video: Stephen Meyer - Functional Proteins And Information For Body Plans - video https://vimeo.com/91322260bornagain77
June 7, 2014
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Piotr, since wd400 refuses to address the evidence on its merits, perhaps you can give me a clue. Why is it so important for you to believe that neo-Darwinian processes generated humans in spite of the fact that neo-Darwinian processes are shown to be grossly inadequate of accomplishing such a transformation in form?
Dr. Stephen Meyer comments at the end of the preceding video,,, ‘Now one more problem as far as the generation of information. It turns out that you don’t only need information to build genes and proteins, it turns out to build Body-Plans you need higher levels of information; Higher order assembly instructions. DNA codes for the building of proteins, but proteins must be arranged into distinctive circuitry to form distinctive cell types. Cell types have to be arranged into tissues. Tissues have to be arranged into organs. Organs and tissues must be specifically arranged to generate whole new Body-Plans, distinctive arrangements of those body parts. We now know that DNA alone is not responsible for those higher orders of organization. DNA codes for proteins, but by itself it does not insure that proteins, cell types, tissues, organs, will all be arranged in the body. And what that means is that the Body-Plan morphogenesis, as it is called, depends upon information that is not encoded on DNA. Which means you can mutate DNA indefinitely. 80 million years, 100 million years, til the cows come home. It doesn’t matter, because in the best case you are just going to find a new protein some place out there in that vast combinatorial sequence space. You are not, by mutating DNA alone, going to generate higher order structures that are necessary to building a body plan. So what we can conclude from that is that the neo-Darwinian mechanism is grossly inadequate to explain the origin of information necessary to build new genes and proteins, and it is also grossly inadequate to explain the origination of novel biological form.’ Stephen Meyer - (excerpt taken from Meyer/Sternberg vs. Shermer/Prothero debate - 2009) Darwin's Doubt narrated by Paul Giem - The Origin of Body Plans - video http://www.youtube.com/watch?list=PLHDSWJBW3DNUaMy2xdaup5ROw3u0_mK8t&v=rLl6wrqd1e0&feature=player_detailpage#t=290
The empirical evidence simply refuses to cooperate with Darwinists. Thus Piotr, since you have no evidence to support you belief that such a transformation is possible by unguided Darwinian processes, why is it so important for to believe that it did happen by unguided Darwinian processes?bornagain77
June 7, 2014
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Pav wrote: 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? Yes something like that thanks. I think though upon reflection, that the example given wouldn't perhaps read different as to its triplet translation, or should I say that no one including Dr Tomkins is saying it will. How the deletions and indels are identified and not confused in translation beats me, please if anyone can and wants to explain I'm all ears. I think that if Dr Tomkins did deign to take a look at the 'gene' wd400 proposed, he would agree on the 98% similarity. But what Dr Tomkins seems to be saying to me (I will have to re-read some stuff to be sure), is that the deletions and indels actually add up to cause an 85% similarity only; this when only comparing protein coding regions, as was claimed of the original human / chimp analysis. But Dr Tomkins compares other factors of the genomes as well, which then further reduces the similarity to the average of 70%. Are these other regions or are they other differences within the protein coding area of the genome? What do you think people? Whatever view is taken as to the strong similarities, the differences must be explained by some mechanism though.willh
June 7, 2014
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wd400: It's a good thing Tomkins doesn't write plagiarism detection software. If someone copied a whole book (say, 200 pages of text) and then omitted a letter or inserted a comma once per page, Tomkins's method would demonstrate that the original and the copy ale less than 1% similar.Piotr
June 7, 2014
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Of related interest, in post 129 wd400 states:
"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."
Which is interesting since that 70% figure, besides turning up in Dr. Tomkins analysis of chimp and human genomes, also turned up here:
Family Ties: Completion of Zebrafish Reference Genome Yields Strong Comparisons With Human Genome – Apr. 17, 2013 Excerpt: Researchers demonstrate today that 70 per cent of protein-coding human genes are related to genes found in the zebrafish,,, http://www.sciencedaily.com/releases/2013/04/130417131725.htm
If that was not bad enough, a few months ago it was found:
Shark and human proteins “stunningly similar”; shark closer to human than to zebrafish – December 9, 2013 Excerpt: “We were very surprised to find, that for many categories of proteins, sharks share more similarities with humans than zebrafish,” Stanhope said. “Although sharks and bony fishes are not closely related, they are nonetheless both fish … while mammals have very different anatomies and physiologies. https://uncommondescent.com/intelligent-design/shark-and-human-proteins-stunningly-similar-shark-closer-to-human-than-to-zebrafish/
Of course wd400 will throw out words such as 'conserved' and 'convergent' and wax poetic as to how the changes did and did not occur, with NEVER an empirical demonstration of what he claims, but the plain fact of the matter is that findings such as these (of which there are many more examples which could be cited) are not expected from basic Darwinian presuppositions. ,,, contradictory findings All of which goes deeper into the issue of the non-falsifiability of the Darwinian hypothesis. i.e. no matter what finding, Darwinists, since Darwinism has no demarcation criteria so as to separate it as a true science instead of a pseudo-science, are always able to make up a 'just so' story as to why it is not a problem for their beloved theory.bornagain77
June 7, 2014
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Moreover, in regards to calling into question wd400's assertion of 98% similarity, number 1, it is interesting to note how extremely complex the gene actually is now compared to just a decade ago:
The Extreme Complexity of A Gene - Raymond Bohlin - video http://www.metacafe.com/watch/8593991/
Also of note at the end of the video Dr. Bohlen states:
“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
and number 2, the genomes are not 98% similar: Humans and chimps have 95 percent DNA compatibility, not 98.5 percent, research shows – 2002 Excerpt: Genetic studies for decades have estimated that humans and chimpanzees possess genomes that are about 98.5 percent similar. In other words, of the three billion base pairs along the DNA helix, nearly 99 of every 100 would be exactly identical. However, new work by one of the co-developers of the method used to analyze genetic similarities between species says the figure should be revised downward to 95 percent. http://www.caltech.edu/content/humans-and-chimps-have-95-percent-dna-compatibility-not-985-percent-research-shows Guy Walks Into a Bar and Thinks He’s a Chimpanzee: The Unbearable Lightness of Chimp-Human Genome Similarity – 2009 Excerpt: One can seriously call into question the statement that human and chimp genomes are 99% identical. For one thing, it has been noted in the literature that the exact degree of identity between the two genomes is as yet unknown (Cohen, J., 2007. Relative differences: The myth of 1% Science 316: 1836.). ,,, In short, the figure of identity that one wants to use is dependent on various methodological factors. http://www.evolutionnews.org/2009/05/guy_walks_into_a_bar_and_think.html as to biased methodological factors of Darwinists: Genome-Wide DNA Alignment Similarity (Identity) for 40,000 Chimpanzee DNA Sequences Queried against the Human Genome is 86–89% – Jeffrey P. Tomkins – December 28, 2011 Excerpt: A common claim that is propagated through obfuscated research publications and popular evolutionary science authors is that the DNA of chimpanzees or chimps (Pan troglodytes) and humans (Homo sapiens) is about 98–99% similar. A major problem with nearly all past human-chimp comparative DNA studies is that data often goes through several levels of pre-screening, filtering and selection before being aligned, summarized, and discussed. Non-alignable regions are typically omitted and gaps in alignments are often discarded or obfuscated. In an upcoming paper, Tomkins and Bergman (2012) discuss most of the key human-chimp DNA similarity research papers on a case-by-case basis and show that the inclusion of discarded data (when provided) actually suggests a DNA similarity for humans and chimps not greater than 80–87% and quite possibly even less (70%). http://www.answersingenesis.org/articles/arj/v4/n1/blastin And that is not even taking into consideration the over 1000 completely unique ORFan genes. Thus, why is it so important for wd400 to continue to propagate the myth that chimps and humans are 98% identical. Well although I have no clue as to what motivates wd400 to be so unfair in his treatment of the evidence, my first hunch is that the 98% similarity myth is the only game in town for wd400. Empirically speaking, He simply has nothing else to appeal to. Empirically, He cannot even account for the fixation of two coordinated 'beneficial' mutations much less a massive overhaul of the genomic architecture and structure. A False Trichotomy Excerpt: The common chimp (Pan troglodytes) and human Y chromosomes are “horrendously different from each other”, says David Page,,, “It looks like there’s been a dramatic renovation or reinvention of the Y chromosome in the chimpanzee and human lineages.” https://uncommondescent.com/intelligent-design/a-false-trichotomy/bornagain77
June 7, 2014
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Dr. Tomkins, states this in regards to 'amateur armchair analysis': "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 7, 2014
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wd400, what more proof do you need that they do not share a common ancestor?Mung
June 6, 2014
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Just for fun - blasting all of chromosome 22 against all of chimp chrom. 22. The longest Tomkins hit is 7910bp out of 51304566. The human and chimp genomes are only ~0.00154% similar by this measure!wd400
June 6, 2014
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In the case of a psuedogene, my analysis would be along these lines: there is an 'insertion' that takes place along the length of the sequence which has the effect of disrupting slightly, or more likely, more than slightly the 'binding' of the resulting RNA sequence, which is likely part of the regulatory function of pseudogenes. In this case, I would then accept the 98% figure.PaV
June 6, 2014
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It's not about assumptions, it's about those two sequences. I find it really hard to imagine anyone can really think they are 60% similar. But even if you grant that they are, it shows how little Tomkins 70% numbers mean, and that they don't contradict the 98% number everyone else who looks at these sequences arrives at. PAV, I wasn't talking about his GULO paper, which is apparently contaminated by the same method. But GULO is a psedeudogene full of in-frame stops so not coding. And most of the non-coding portion of the genome is not conserved within- or between species, so sequence changes evidently make little or no difference.wd400
June 6, 2014
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littlejohn: I don't think that it's only a matter of accepting or rejecting some kind of common ancestry; rather, it's about the importance of not only the 'kind' of nucleotide at a particular location, but the location itself: both are important. wd400: Let's remember that Tomkins' study has to do with exon areas in the GULO region; so, it's not non-coding DNA. Nonetheless, as I've pointed out, even if it's 'nc' the locations become important.PaV
June 6, 2014
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The difference of opinion seems to be a matter of perspective (or preference) of how the alignment is interpreted. In order to attain 98% alignment, the insert must be deleted, and the deletion is justified if we assume the sequences have a common ancestor. However, in the absence of any assumptions regarding the origin of the sequences (and the subsequent deletion), the alignment is only 60% similar.littlejohn
June 6, 2014
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Take the top line of your sequence string, then reverse it completely. Per your logic, they are 100% identical. Why? Because you're making the location along the string immaterial.PaV
June 6, 2014
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Lol.wd400
June 6, 2014
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They are 60% similar.PaV
June 6, 2014
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Are those sequences, as typed above, 60% similar? Is it so hard for someone to for at least one anti-evolutionist to go against one of their fellow travellers?wd400
June 6, 2014
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wd400:
…But the sequences are not 60% similar…
Which are not? The nucleotide or the a.a. sequence?
. . . and the same rules will apply to the 98% of the genome that never get made into proteins. So…
Well, if it's the 98% that doesn't code, then it might be just as bad, or even worse. Let's remember, the cellular chemistry that's involved here does not 'know' that the last part of the nucleotide sequence is 'off by one nucleotide.' If the function of the ncRNA is to 'bind' to some molecular machine of one sort or another, then being one position off---but now 'one position off' along the entire length of the sequence which is off by one---would likely cause considerable problems.PaV
June 6, 2014
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BA77 @73 "having the same proteins show up in widely divergent species is devastating against Darwinian claims because, number one, no one has ever seen unguided processes generate a protein.." And nobody has ever seen a protein (or anything) generated by a non-human intelligence either. So what's your point?Acartia_bogart
June 6, 2014
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PaV asked about the a/a sequences. I'm not going to play a thousand questions with you, especially if you can't answer one simple one. Are those sequences 60% similar?wd400
June 6, 2014
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And what about more than one shift? -QQuerius
June 6, 2014
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I didn't ask you about amino acid sequences. -QQuerius
June 6, 2014
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I should add, if you compare actual amino acid sequences between humans and chimps are > 99% identical so I don't the amino acid sequences are gong to save Tomkinswd400
June 6, 2014
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98%, as I think any reasonable person would...wd400
June 6, 2014
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wd400, A student takes a midterm exam in your class. Unfortunately, she skips a question and she shows you that the multiple choice answers in the second half of the test are all shifted by one. If the student's answers would otherwise have been all correct, what grade would you give her, 60% or 98%? Now, if her answers are not otherwise all correct, but merely better, would you give her the better score? (Attention students, this would make a great app!) And what if she's really pretty? ;-) -QQuerius
June 6, 2014
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...But the sequences are not 60% similar... and the same rules will apply to the 98% of the genome that never get made into proteins. So...wd400
June 6, 2014
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Yes, they're 60% similar if, when translated, they share only 60% of the a.a.s.PaV
June 6, 2014
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Are those two sequences 60% similar?wd400
June 6, 2014
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Nah, the skepticism is general and broad-based. It's the hyper-skepticism that's selective. :)Mung
June 6, 2014
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wd400:
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….
What's the difference between these two statements: 1.) "Small nucleotide differences can make large practical difference[s]." and, 2.) "Small nucleotide differences [can make] 'two sequences' [only] 60% similar." Isn't this a distinction without a difference?PaV
June 6, 2014
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