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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
Well, forgive me for paying scant attention to the links, but I thought we were talking about 'convergence': Convergent sequence evolution between echolocating bats and dolphins - Liu et al (2010) Excerpt: We previously reported that the Prestin gene has undergone sequence convergence among unrelated lineages of echolocating bat [3]. Here we report that this gene has also undergone convergent amino acid substitutions in echolocating dolphins, http://www.cell.com/current-biology/abstract/S0960-9822%2809%2902073-9 Common Design in Bat and Whale Echolocation Genes? - January 2011 Excerpt: two new studies in the January 26th issue of Current Biology, a Cell Press publication, show that bats' and whales' remarkable ability and the high-frequency hearing it depends on are shared at a much deeper level than anyone would have anticipated -- all the way down to the molecular level. http://www.evolutionnews.org/2011/01/common_design_in_bat_and_whale042291.html Here's a figure showing bats and dolphins group together on the same tree based on Prestin sequence comparisons. http://sphotos.xx.fbcdn.net/hphotos-ash3/580955_215152708593734_182588468516825_355811_30197372_n.jpg Bat and Whale Echolocation Genes Point to Common Design - February 2011 - Podcast http://intelligentdesign.podomatic.com/entry/2011-02-21T10_59_16-08_00 Moreover, this finding is unexpected from an evolutionary perspective, yet this finding is exactly what we would expect to find from presupposing a Creator to reuse optimal designs: Convergence Drives Evolution Batty - Fazale Rana - September 2010 Excerpt: convergence make sense if life stems from the work of a Creator. http://www.reasons.org/convergence-drives-evolution-batty Bothersome Bats and Other Pests Disturb the "Tree of Life" - Casey Luskin - December 5, 2012 Excerpt: But this is hardly the only known example of molecular convergent evolution. In his book The Cell's Design, chemist and Darwin-skeptic Fazale Rana reviewed the technical literature and documented over 100 reported cases of convergent genetic evolution. Each case shows an example where biological similarity -- even at the genetic level -- is not the result of inheritance from a common ancestor. http://www.evolutionnews.org/2012/12/bothersome_bats067121.html Convergent evolution seen in hundreds of genes - Erika Check Hayden - 04 September 2013 Excerpt: “These results imply that convergent molecular evolution is much more widespread than previously recognized,” says molecular phylogeneticist Frédéric Delsuc at the The National Center for Scientific Research (CNRS) at the University of Montpellier in France, who was not involved in the study. What is more, he adds, the genes involved are not just the few, obvious ones known to be directly involved in a trait but a broader array of genes that are involved in the same regulatory networks. http://www.nature.com/news/convergent-evolution-seen-in-hundreds-of-genes-1.13679bornagain77
June 1, 2014
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1. These papers aren't about "having the same proteins show up in widely divergent species". 2. actually, I don't know what this means.wd400
June 1, 2014
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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 (Axe), and number 2, evolution is shown to be historically contingent, not convergent(Rana).bornagain77
June 1, 2014
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willh, Any observation is compatabile with special creation or "an intelligence", the claim I was responding to was that shared amino acid changes in these proteins was evidence "against evolution" (and even "devastating" evidence. You can treat most of the maths of that paper as background - they use it to establish that there has been selection for changing amino acid sequences in echolocating species over time (based on the rate of synonomous and non-syn. substitutions in the different groups), and to attempt to reconstruct ancestral sequences.wd400
June 1, 2014
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(Since we’re into breaking rules) That’s not what I was objecting to. Let me put it another way. Attributing similar “selection pressure” as the cause for the evolution of echolocation in two kinds of bats and toothed whales strains credibility when there are many non-echolocating bats and whales, not to mention nocturnal animals, benthic animals such as squid, etc., that did not develop cochlear enhancements (or the “melon” in toothed whales).
But this paper and (piotr comment specifically) is about proteins invlolved in hearing in echolocators, not about why and how echolocation evolved generally.
One would expect the opposite. Supposedly, the evolutionary process was independent and “parallel”
Check out the PLOS Genetics paper - the trees derrived from nucleotide sequences correspond to the species tree; those from protein (i.e. the things that actually contriute to listening) group the echolocators. That's explicable under convergent evolution (the same amino acid changes happening in different ways in each lineage) but hard to explain otherwise. I didn't watch the Tompkins video, but I don't know what "parallel human evolution" would mean, or how his supposed 70% identity could make an argument for it.wd400
June 1, 2014
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Q:
Attributing similar “selection pressure” as the cause for the evolution of echolocation in two kinds of bats and toothed whales strains credibility when there are many non-echolocating bats and whales, not to mention nocturnal animals, benthic animals such as squid, etc., that did not develop cochlear enhancements (or the “melon” in toothed whales).
Different selection pressures, obviously. I don't understand the difficulty you're having with basic biology. If not common ancestry, then common advantage. If not common ancestry nor common advantage, then different environment. A theory that explains everything and predicts nothing. What more could you want?
“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…”
Mung
June 1, 2014
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I'm just amusing myself with Piotr's flawed reasoning, bald assertions, and otherwise clairvoyant abilities demonstrated here. Piotr opens in typical evolutionatry fashion by appealing to majority opinion as unassailable fact:
There are lots of paleontologists who meet this description, and almost all of them disagree with Alan Feduccia.
And now we are into Piotr's full on psychic divination and faith claims:
Ostrom wasn’t right about every detail (and little wonder, considering that he had very scanty data at his disposal), but the core of his hypothesis remains correct: birds are a group nested within Theropoda. Wings are an example of exaptation: feathers developed before flight. They played other functions originally (and, by the way, still play them in modern birds). Flight was not the purpose of bird evolution; it became a fortuitous possibility for some small dinosaurs, and long pennaceous feathers were co-opted to generate aerodynamic lift and thrust.
Piotr please share your crystal ball with us... honestly do you actually believe these imagineered assertions your tossing out are scientific statements? This is laughable...
Because it’s already the descendant of billions of ancestral generations, every single one of them fit enough to leave offspring. If it happens to be additionally the lucky carrier of an innate feature conferring a slight adaptive advantage, it has a slightly better chance of producing offspring with a similar slight advantage.
Actually the more reasonable assumption is that if we hypothetically imagine the appropriate function-finding incremental mutations occurred at all, the vast majority of them would not produce any significant fitness signal that would even be selected for. But I know you guys don't like to think about pesky things like this. You have a magical view of natural selection, Piotr.
There’s no need to speculate; we’ve got the fossils.
lol... Fossils which are interpreted through various rounds of speculation... producing an ambiguous transitional hypothesis that ultimately must win the day by a consensus of subjective opinion as you already demonstrated.
Convergent evolution, no matter how amazing it looks, is hardly big news when it affects an adaptive trait (the ability to echolocate at high frequencies) and involves similar selective pressures in both lineages.
Oh really, and how do you know a "convergent" trait was subject to similar selective pressures? Well because the traits exist of course! And evolution must be true! The circular reasoning of the evolutionist is almost beautiful at times in its simplicity... Thanks for the amusement, Piotr.lifepsy
June 1, 2014
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wd400@53 objected, including
Only three groups of mammals do echolocation well, so it can’t be true that “ay you could make the same argument for any two animals on the planet.”
(Since we're into breaking rules) That's not what I was objecting to. Let me put it another way. Attributing similar "selection pressure" as the cause for the evolution of echolocation in two kinds of bats and toothed whales strains credibility when there are many non-echolocating bats and whales, not to mention nocturnal animals, benthic animals such as squid, etc., that did not develop cochlear enhancements (or the "melon" in toothed whales).
Moreover, Convergent evolution is not being offered as an ad hoc justification for the similarity of these sequences, it’s what was being tested. It is suprising (to me at least) that the convergence is strong enough to make the protein-trees diverge from the true history of the species but not, as you claim “devestating.
One would expect the opposite. Supposedly, the evolutionary process was independent and "parallel" (as the authors of the paper indicated in their abstract), especially considering the differences in underwater hearing. Or maybe all three animals arrived at the top of Mount Really Improbable at the same time, paraphrasing Dawkins. According to bornagain77's link (https://vimeo.com/95287522), considering the revision to about 70% similarity between chimpanzees and humans claimed by Jeffrey Tomkins, along with the evidence against fusion on chromosome 2 of humans, if true, would likewise open the door to parallel human evolution. If not, what else? Did you see the Miller quote? -QQuerius
June 1, 2014
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wd400 wrote: Can you explain (without a torrent of links and quotes…) how the shared amino-acids genes associated with hearing in bats and toothed-whales “contradicts” evolution. Especially given the fact the nucleotide sequence of the genes coding for these proteins matches the species tree? The paper you linked to at your #53 post does confirm the phylogenetic tree's expected, once the echolocation related genetic changes are dropped. Is there a question that genetic similarities, posited in the phylogenetic tree's, wouldn't concur in special creation? The noted genetic changes that allow both echo locating bats and dolphins this specific ability, coupled with the same singular gene expressions, can also be explained by a directed change. That change can be accomplished by an intelligence and not a natural cause only. In the linked paper no specific process of natural causes, for this 'parallel' evolution in the genes for echolocation, was discussed in detail. Any nod to the powers of selection or the ability of ideal mutations being assumed? Or is there some other mechanism? It really only seemed to me to outline in general, the argument between the content of evolutionary development [convergent, parallel and co evolution]. The maths of it seemed to be used to prove, that indeed a striking convergent / parallel evolutionary process has occurred. But I must admit, these kind of calculations are not my daily fare; any assistance in understanding this aspect is appreciated.willh
June 1, 2014
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Piotr, I assume your position is Darwinian since you do indeed defend Darwinian claims so dogmatically, (if you are more of a Shapiro or Kaufman type evolutionist please clarify, i.e. natural genetic engineering, and self organization respectfully) ,,, but to clearly illustrate just how far removed from empirical science the 'Darwinian' position actually is, there is not one iota of empirical evidence that Darwinian processes can generate any non-trivial levels of functional information/complexity above that which is already present in life:
The Law of Physicodynamic Insufficiency - Dr David L. Abel - November 2010 Excerpt: “If decision-node programming selections are made randomly or by law rather than with purposeful intent, no non-trivial (sophisticated) function will spontaneously arise.”,,, After ten years of continual republication of the null hypothesis with appeals for falsification, no falsification has been provided. The time has come to extend this null hypothesis into a formal scientific prediction: “No non trivial algorithmic/computational utility will ever arise from chance and/or necessity alone.” http://www-qa.scitopics.com/The_Law_of_Physicodynamic_Insufficiency.html “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain - Michael Behe - December 2010 Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain. http://behe.uncommondescent.com/2010/12/the-first-rule-of-adaptive-evolution/ Michael Behe talks about the preceding paper on this podcast: Michael Behe: Challenging Darwin, One Peer-Reviewed Paper at a Time - December 2010 http://intelligentdesign.podomatic.com/player/web/2010-12-23T11_53_46-08_00 Scant search for the Maker Excerpt: But where is the experimental evidence? None exists in the literature claiming that one species has been shown to evolve into another. Bacteria, the simplest form of independent life, are ideal for this kind of study, with generation times of 20 to 30 minutes, and populations achieved after 18 hours. But throughout 150 years of the science of bacteriology, there is no evidence that one species of bacteria has changed into another, in spite of the fact that populations have been exposed to potent chemical and physical mutagens and that, uniquely, bacteria possess extrachromosomal, transmissible plasmids. Since there is no evidence for species changes between the simplest forms of unicellular life, it is not surprising that there is no evidence for evolution from prokaryotic to eukaryotic cells, let alone throughout the whole array of higher multicellular organisms. - Alan H. Linton - emeritus professor of bacteriology, University of Bristol. http://www.timeshighereducation.co.uk/story.asp?storycode=159282 Where's the substantiating evidence for neo-Darwinism? https://docs.google.com/document/d/1q-PBeQELzT4pkgxB2ZOxGxwv6ynOixfzqzsFlCJ9jrw/edit
Now Piotr, it is not a matter of Darwinism having some empirical basis and Darwinists working from that established basis, but it is a matter of Darwinism having no empirical basis whatsoever in which to work from, and yet having Darwinists pretend as if they have a empirical basis in which to make their sweeping assumptions for how all life on earth arose.,,, Thus my quip of Darwinists ‘having both feet planted firmly in mid-air’ empirically speaking. In other words, It is not me that undermines any integrity Darwinists may have had in making their sweeping claims for how all life arose but it is the empirical evidence itself which undermines any intgity they might have had in their claims. As Berlinski says of Darwinists, 'you guys simply are not credible'. Dogs stay dogs- Dr. David Berlinski - On Evolution https://www.youtube.com/watch?v=9Yk9BO9WzIsbornagain77
June 1, 2014
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ba77: LOL, anyone who criticises Tomkins must be a "neo-Darwinist", and so can't be trusted (whatever the argument). That makes Tomkins invincible -- but of course only in your eyes, which is a lame consolation.Piotr
June 1, 2014
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Piotr, I disagree wholeheartedly. and hold AoS to be flawed in his analysis. The one thing that my years of dealing with neo-Darwinists has taught me is to never trust anything they say. And you, true to your Darwinian roots, ignore the fact, as I have shown, that you have no empirical basis for Darwinism in which to justify making extrapolations of genetic similarity/dissimilarity in the first place. But regardless of 'having both feet planted firmly in mid-air' empirically speaking, you feel qualified to pronounce on what Darwinism did and did not produce.... It would be hilarious if not for the fact that you think you are actually being rational in all this!bornagain77
June 1, 2014
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ba77: AoS did a very careful analytic job and wrote a detailed review exposing all the weaknesses of Tomkins's methodology. Tomkins did not really address any of his points. He only waved away the criticism, accusing AoS of general amateurishness and sloppy reading, and wound the post up with an assurance that his paper was accurate in all respects. This is not an acceptable reply to a devastating review. But then, how would you know?Piotr
June 1, 2014
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Querius:
That’s odd. The scientists who discovered the biochemical similarity apparently were amazed. I wonder why.
Were they really amazed? http://tinyurl.com/qdavzqm They only comment upon the fact that such a degree of molecular convergence is exceptionally rare (which it probably is). My impression is that they were pleased rather than disturbed by their discovery. Do try to understand what wd400 says about the match between nucleotide substitutions and the species family tree. It's an important point.Piotr
June 1, 2014
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Moreover Piotr, aside from the detailed genetic analysis which overturned evolutionary assumptions, I note that you, nor any other atheistic neo-Darwinist, has any empirical evidence that supposed beneficial mutations can fix in a genome: The Real Barrier to Unguided Human Evolution - Ann Gauger - April 25, 2012 Excerpt: Their results? They calculated it would take six million years for a single base change to match the target and spread throughout the population, and 216 million years to get both base changes necessary to complete the eight base binding site. Note that the entire time span for our evolution from the last common ancestor with chimps is estimated to be about six million years. Time enough for one mutation to occur and be fixed, by their account. http://www.evolutionnews.org/2012/04/the_real_barrie058951.html Experimental Evolution in Fruit Flies (35 years of trying to force fruit flies to evolve in the laboratory fails,,, spectacularly) - October 2010 Excerpt: "Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles.,,, "This research really upends the dominant paradigm about how species evolve," said ecology and evolutionary biology professor Anthony Long, the primary investigator. http://eebweb.arizona.edu/nachman/Suggested%20Papers/Lab%20papers%20fall%202010/Burke_et_al_2010.pdf supplemental note: Fruit fly with the wings of beauty – July 2012 Excerpt: But a closer examination of the transparent wings of Goniurellia tridens reveals a piece of evolutionary(?) art. Each wing carries a precisely detailed image of an ant-like insect, complete with six legs, two antennae, a head, thorax and tapered abdomen. http://www.thenational.ae/news/uae-news/science/fruit-fly-with-the-wings-of-beautybornagain77
June 1, 2014
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Piotr, Dr. Tomkins, further down from the very comment you cited, was kind enough to respond to the 'hatchet job' against the integrity of his work: 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 1, 2014
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bornagain77 @58 May I remind you that Tomkins's incompetence was exposed on this very blog? https://uncommondescent.com/human-evolution/evolutionary-convergence-saves-creationist-hypothesis-over-gulo/#comment-498380Piotr
June 1, 2014
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a primary example of evolutionary assumptions giving a tree-like pattern and detailed analysis evaporating the tree-like pattern is in the 98% genetic similarity myth: The Myth of 98% Genetic Similarity between Humans and Chimps - Jeffrey Tomkins PhD. - video https://vimeo.com/95287522bornagain77
June 1, 2014
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In this following recent podcast, Dr. Meyers, at the 15:25 minute mark, talks about how computer algorithms are set up to 'generate a tree-like pattern': "The computer programs that analyze the sequence similarities, or differences, are programmed in advance to generate a tree-like pattern. In other words, the assumption of a common ancestor is built into the way in which the analysis is performed. So there is no way you would get anything other than the conclusion,,, It's a question begging assumption." Stephen Meyer - on the Cambrian Explosion - podcast http://intelligentdesign.podomatic.com/entry/2014-05-30T17_33_15-07_00 Disagree with him? well,,, Pattern pluralism and the Tree of Life hypothesis - 2006 Excerpt: Hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so, but at its base the universal TOL rests on an unproven assumption about pattern that, given what we know about process, is unlikely to be broadly true. http://www.pnas.org/content/104/7/2043.abstract Moreover, when the data is analyzed in detail, instead of by algorithms 'designed' to draw a tree-like out for you, the tree-like pattern disappears: Why Darwin was wrong about the (genetic) tree of life: - 21 January 2009 Excerpt: Syvanen recently compared 2000 genes that are common to humans, frogs, sea squirts, sea urchins, fruit flies and nematodes. In theory, he should have been able to use the gene sequences to construct an evolutionary tree showing the relationships between the six animals. He failed. The problem was that different genes told contradictory evolutionary stories. This was especially true of sea-squirt genes. Conventionally, sea squirts - also known as tunicates - are lumped together with frogs, humans and other vertebrates in the phylum Chordata, but the genes were sending mixed signals. Some genes did indeed cluster within the chordates, but others indicated that tunicates should be placed with sea urchins, which aren't chordates. "Roughly 50 per cent of its genes have one evolutionary history and 50 per cent another," Syvanen says. ."We've just annihilated the tree of life. It's not a tree any more, it's a different topology entirely," says Syvanen. "What would Darwin have made of that?" http://www.newscientist.com/article/mg20126921.600-why-darwin-was-wrong-about-the-tree-of-life.html I would like to point out that this, 'annihilation' of Darwin's genetic tree of life, article came out on the very day that Dr. Hillis, a self-proclaimed 'world leading expert' on the genetic tree of life, testified before the Texas State Board Of Education that the genetic tree of life overwhelmingly confirmed gradual Darwinian evolution. One could almost argue it was 'Intelligently Designed' for him to exposed as a fraud on that particular day of his testimony instead of just any other day of the year.bornagain77
June 1, 2014
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wd400, but alas a rule is a rule.bornagain77
June 1, 2014
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OK, I'll break a rule and answer one of your posts...
,,, The one predictable thing about evolution is that if you point out one of the many evidences that contradict evolution
Can you explain (without a torrent of links and quotes...) how the shared amino-acids genes associated with hearing in bats and toothed-whales "contradicts" evolution. Especially given the fact the nucleotide sequence of the genes coding for these proteins matches the species tree?wd400
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wd400 states: 'you failed to understand' ,,, The one predictable thing about evolution is that if you point out one of the many evidences that contradict evolution then a Darwinist will eventually come along and say "you just don't understand evolution" for instance: “Die, Selfish Gene … “ science writer just “doesn’t understand” genetic evolution – Harvard psychologist https://uncommondescent.com/intelligent-design/die-selfish-gene-science-writer-just-doesnt-understand-genetic-evolution-harvard-psychologist/bornagain77
June 1, 2014
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Querius. I think you failed to understand what's going on in these papers. THey are looking specifically and proteins associated with hearing in mammals. Only three groups of mammals do echolocation well, so it can't be true that "ay you could make the same argument for any two animals on the planet." Moreover, Convergent evolution is not being offered as an ad hoc justification for the similarity of these sequences, it's what was being tested. It is suprising (to me at least) that the convergence is strong enough to make the protein-trees diverge from the true history of the species but not, as you claim "devestating. In fact, check out his follow up paper in which trees estimate from DNA sequences find the species tree, while protein sequences group echolocaters. How can you explain that pattern if not through convergent amino-acid substitutions in each lineage?wd400
June 1, 2014
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Piotr,
Convergent evolution, no matter how amazing it looks, is hardly big news when it affects an adaptive trait (the ability to echolocate at high frequencies) and involves similar selective pressures in both lineages.
That's odd. The scientists who discovered the biochemical similarity apparently were amazed. I wonder why. If you think whales and bats had similar selective pressures, than I'd say you could make the same argument for any two animals on the planet. Presumably, the squid eaten by the toothed whales also have had similar selective pressures for millions of years, yet they don't have biosonar.
It would be more surprising to see non-adaptive innovations shared by bats and cetaceans, such as orthologous ERVs.
No, it wouldn't. The supposed ERVs would simply not be recognized as such. The theory of evolution can explain anything, but successfully predicts nothing. -QQuerius
June 1, 2014
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wd400:
Lamarck’ theory had animals striving toward some goal (so I guess he’d have therapods really wanting to fly).
Really? So facile an answer. Here's QuickWiki on Lamarckism:
Giraffes stretching their necks to reach leaves high in trees (especially Acacias), strengthen and gradually lengthen their necks. These giraffes have offspring with slightly longer necks (also known as "soft inheritance").
I don't see that they anywhere say that the giraffes "wanted longer necks," do you? Would you like to update your post?PaV
June 1, 2014
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Querius: Convergent evolution, no matter how amazing it looks, is hardly big news when it affects an adaptive trait (the ability to echolocate at high frequencies) and involves similar selective pressures in both lineages. It would be more surprising to see non-adaptive innovations shared by bats and cetaceans, such as orthologous ERVs.Piotr
June 1, 2014
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Wow, bornagain77. The whale-bat evolutionary connection is amazing! I had no idea that their common echolocation ability was so remarkably similar even on a molecular level. So, I'm sure that even Piotr would have difficulty swallowing an evolutionary sequence between bats and toothed whales . . . or is it the other way around?. The MRCA between hippopotamus and Indohyus is precisely the evolutionary age of bats! Coincidence?
Remarkably, prestin amino-acid sequences of echolocating dolphins have converged to resemble those of distantly related echolocating bats. ... Even more remarkable is the new finding that echolocating dolphins and porpoises show Prestin gene sequences that resemble those of echolocating bats. Whales and dolphins belong to the order Cetartiodactyla, and their closest living relatives may be hippopotamuses. Nevertheless, dolphins and porpoises share at least 14 derived amino acid sites in prestin with echolocating bats, including 10 shared with the highly specialised CF bats. Consequently, dolphins and porpoises form a sister group to CF bats in a phylogenetic analysis of prestin sequences (Figure 1). This finding is arguably one of the best examples of convergent molecular evolution discovered to date, and is exceptional because it is likely to be adaptive, driven by positive selection. (Gareth Jones, "Molecular Evolution: Gene Convergence in Echolocating Mammals," Current Biology, Vol. 20(2):R62-R64 (January, 2010) (internal citations removed).)
In the face of devastating evidence, Darwinists turn it around to say that it's the "one of the best examples" for convergent evolution! They even dragged hippos into the mix! And what a mess they'd make if they could fly--duck for cover, everyone!!! Or maybe the supposed "wolf-like" ancestor of the whale evolved echolocation in the dark forest biome that it inhabited, and then had the foresight to bring it along to its benthic destination. So I guess there shouldn't be any problem if someone claimed the similarity between humans and chimps was an Even Better Example of convergent evolution! Again, the theory of evolution can explain anything, but successfully predicts nothing. -QQuerius
May 31, 2014
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This is just too much..my sides ache from all the laughing I've done reading some of these comments haha, thanks folks. Piotr, sounds like you're a true believer, praise Darwin hallelujah. Some healthy skepticism is in order I think. Reading your posts only serves to show how insanely wedded to your belief system you are. Your faith is hampering your objectivity and is affecting your ability to think critically.humbled
May 31, 2014
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Bat Evolution? - No Transitional Fossils! - video (w/notes) http://www.metacafe.com/watch/6003501/bornagain77
May 31, 2014
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Bird Evolution vs. The Actual Fossil Evidence - video and notes http://vimeo.com/30926629 The Unknown Origin of Pterosaurs - video http://www.youtube.com/watch?v=XP6htc371fM ------------ FLIGHT: The Genius of Birds - Flight muscles - video http://www.youtube.com/watch?v=aFdvkopOmw0 FLIGHT: The Genius of Birds - Skeletal system - video http://www.youtube.com/watch?v=11fZS_B6UW4 FLIGHT: The Genius of Birds - Embryonic Development - video http://www.youtube.com/watch?v=-Ah-gT0hTtobornagain77
May 31, 2014
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