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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
"the history of mankind, there has ever been a cult so pathologically cretinous" but what are you REALLY trying to say Axel? :)bornagain77
June 11, 2014
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'In that regard, one might argue that they are more illogically-emotional nihilists (Spock suffering a bout of the vapours, as it were), rather than religious devotees.' I mean, of course, the emotional nihilists.Axel
June 11, 2014
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I believe you said, BA, that the materialist cultists believe we've come to the end of science, and I believe that they're substantially correct in terms of its approach to metaphysics, but like pre-civilised (before building urban agglomerations) hunter-gatherer types, they identify the end, but have not identified the means that brought them to it. Indeed, as you pointed out, QM is the ultimate, physical paradigm. Although hunter-gatherers show a more disciplined intellectual approach to their religions, not going to pieces with wild fantasies. In that regard, one might argue that they are more illogically emotional nihilists (Spock suffering a bout of the vapours, as it were), rather than religious devotees. I very much doubt whether in the history of religion, indeed, the history of mankind, there has ever been a cult so pathologically cretinous that its adherents believe (and seek to explain...) that, once upon a time, nothing turned itself into everything.Axel
June 11, 2014
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Acartia_bogart @211
But, for the sake of argument, let’s assume that Tomkins approach is valid and the % similarity between chimps and humans is less that the 98% that was previously thought. It is reasonable to assume that comparisons between the genetics of other species would suffer the same fate (i.e., lower the % similarity numbers between any two species that was previously looked at). The logical conclusion would be that chimps are still the closest relative to humans. So, nothing has changed.
I basically agree, with the following reservation: greater similarity (whether molecular or morphological) does not necessarily correspond to closer relatedness. Let's imagine that a clade conatins three taxa, A, B, and C, and that its structure is as follows: (A (B C)). Now let's imagine that the evolution of C was for some reason accelerated in comparison with A and B (for example, as a result of colonising a new habitat, with strong selective pressures, or some dramatic genomic event, e.g. a whole genome duplication). As a result, the more conservative taxa A and B will be more "similar" to each other than either is to C, although they aren't more closely related. For determining historical relationships, what matters is that B and C share some common innovations not shared with A, and A exhibits its own unique innovations not shared with B or C. The nested hierarchy is still there.Piotr
June 11, 2014
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Of related note to 'form' falsifying Darwinian claims: Darwin's Finches Show Rule-Constrained Variation in Beak Shape - June 10, 2014 Excerpt: A simple yet powerful mathematical rule controls beak development, Harvard scientists find, while simultaneously preventing beaks from evolving into something else.,,, We find in Darwin's finches (and all songbirds) an internal system, controlled by a non-random developmental process. It is flexible enough to allow for variation, but powerful enough to constrain the beak to its basic form (a conical shape modulated by scaling and shear) so that the rest of the bird's structures are not negatively affected. Beak development is controlled by a decay process that must operate at a particular rate. It's all very precise, so much so that it could be modeled mathematically.,,, The very birds that have long been used as iconic examples of natural selection become, on closer examination, paragons of intelligent design. http://www.evolutionnews.org/2014/06/darwins_finches086581.htmlbornagain77
June 11, 2014
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And not so surprisingly, protein folding is also notorious for keeping supercomputers busy for days: “Blue Gene’s final product, due in four or five years, will be able to “fold” a protein made of 300 amino acids, but that job will take an entire year of full-time computing.” Paul Horn, senior vice president of IBM research, September 21, 2000 http://www.news.com/2100-1001-233954.html Networking a few hundred thousand computers together has reduced the time to a few weeks for simulating the folding of a single protein molecule: A Few Hundred Thousand Computers vs. A Single Protein Molecule – video https://www.youtube.com/watch?v=lHqi3ih0GrI Of related note: The Humpty-Dumpty Effect: A Revolutionary Paper with Far-Reaching Implications – Paul Nelson – October 23, 2012 Excerpt: Put simply, the Levinthal paradox states that when one calculates the number of possible topological (rotational) configurations for the amino acids in even a small (say, 100 residue) unfolded protein, random search could never find the final folded conformation of that same protein during the lifetime of the physical universe. http://www.evolutionnews.org/2012/10/a_revolutionary065521.html And as with DNA repair, and not so surprisingly, protein folding is found to belong to the quantum world, not to the ‘classical’ world: Physicists Discover Quantum Law of Protein Folding – February 22, 2011 Quantum mechanics finally explains why protein folding depends on temperature in such a strange way. Excerpt: First, a little background on protein folding. Proteins are long chains of amino acids that become biologically active only when they fold into specific, highly complex shapes. The puzzle is how proteins do this so quickly when they have so many possible configurations to choose from. To put this in perspective, a relatively small protein of only 100 amino acids can take some 10^100 different configurations. If it tried these shapes at the rate of 100 billion a second, it would take longer than the age of the universe to find the correct one. Just how these molecules do the job in nanoseconds, nobody knows.,,, Their astonishing result is that this quantum transition model fits the folding curves of 15 different proteins and even explains the difference in folding and unfolding rates of the same proteins. That’s a significant breakthrough. Luo and Lo’s equations amount to the first universal laws of protein folding. That’s the equivalent in biology to something like the thermodynamic laws in physics. http://www.technologyreview.com/view/423087/physicists-discover-quantum-law-of-protein/ Another factor severely complicating man’s ability to properly mimic protein folding is that, much contrary to evolutionary thought, many proteins are ‘context dependent’ and fold differently in different ‘molecular situations’: The Gene Myth, Part II – August 2010 Excerpt: the rate at which a protein is synthesized, which depends on factors internal and external to the cell, affects the order in which its different portions fold. So even with the same sequence a given protein can have different shapes and functions. Furthermore, many proteins have no intrinsic shape, taking on different roles in different molecular contexts. So even though genes specify protein sequences they have only a tenuous influence over their functions. http://darwins-god.blogspot.com/2010/08/gene-myth-part-ii.html How all this plays out is investigated here: Origin of life: A problem in the origin of information – April 2014 Excerpt: A hallmark of life is the way information flows between different levels of organization. In non-living systems, information flows from the bottom up–the properties of the individual parts determine the fate of the system. But with living systems, that flow goes both ways. Not only genes dictate the nature of proteins which in turn affect the functioning of cells, tissues and organisms, but the behavior of proteins, cells, and organisms also control gene expression. This is what Walker calls “top-down control” or “top-down causation.” And to Walker, this transition–from information seeping upward only to information flowing both up and down–is the key to understanding life’s origins. Put differently, the blueprint for building an organism isn’t stored in its DNA only, but it’s distributed in the state of the entire system. Dr. Sara Walker https://uncommondescent.com/intelligent-design/origin-of-life-a-problem-in-the-origin-of-information/ ‘Top down’ causation is antithetical to basic Darwinian precepts: Intelligent Design Might Be Wrong, But Not the Way You Think by Stephen H. Webb – February 2014 Excerpt: Darwin, like all moderns, believed that matter was something particular, that matter is composed of small bits of stuff called atoms, and thus it can be pushed from behind, as it were, without being pulled from beyond, by form. http://www.firstthings.com/web-exclusives/2014/02/occasionalism-intelligent-design-and-the-myth-of-secondary-causation Verse, Quote, and Music: Psalm 139:15 My frame was not hidden from you when I was made in the secret place, when I was woven together in the depths of the earth. “Now the world appears to be divided into two realms, described by two different sets of physical laws. The quantum (world),, which is immaterial, coexisting possibilities, non-local, unified, connected, has some ultimate truth although we don’t know what it is yet, deeper levels of reality, and in many senses ‘spirit-like’. The classical world, the (illusory) billiard ball universe that we (appear to) live in right now, but not so, is material, Newtonian, definite, macroscopic, local, predictable, disconnected, post-modern, and somewhat boring actually. Now, what is life? If you approach life from classical physics, you see that biology is a set of self-organizing functions. There is no secret to life. Brain activities are equivalent to computers, consciousness is a epi-phenomenal illusion with no causal power. That’s the party line in standard neuroscience and philosophy. Accordingly, Thomas Huxley said years ago, ‘We are merely conscious automaton,’ helpless spectators., That’s the story we get from classical physics approach to the brain. Now,, applying quantum physics to biology, first by Erwin Schrodinger,,, quantum features (of biology include), non-local entanglement, super-position, unity, quantum coherence, quantum information. A kind of quantum vitalism, may play key roles in biological function.,,,” Stuart Hameroff – Does Quantum Biology Support A Quantum Soul? – video https://vimeo.com/29895068 High School Musical 2 – You are the music in me http://www.youtube.com/watch?v=IAXaQrh7m1obornagain77
June 11, 2014
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Acartia_bogart although I'm pretty sure it is pointless to show you and wd400, both dogmatic atheists who IMHO could care less about what the evidence actually says, that there is empirical evidence for God creating the DNA molecule, none-the-less, to show that Theistic premises are up to the benchmark of testability and that atheistic/materialistic premises are not, I will show you (and onlookers) anyway: DNA repair is a fascinating process to learn about. One facet of the process is highlighted here: Quantum Dots Spotlight DNA-Repair Proteins in Motion – March 2010 Excerpt: “How this system works is an important unanswered question in this field,” he said. “It has to be able to identify very small mistakes in a 3-dimensional morass of gene strands. It’s akin to spotting potholes on every street all over the country and getting them fixed before the next rush hour.” Dr. Bennett Van Houten – of note: A bacterium has about 40 team members on its pothole crew. That allows its entire genome to be scanned for errors in 20 minutes, the typical doubling time.,, These smart machines can apparently also interact with other damage control teams if they cannot fix the problem on the spot. http://www.sciencedaily.com/releases/2010/03/100311123522.htm What is interesting is that DNA repair machines ‘Fixing every pothole in America before the next rush hour’ is analogous to the traveling salesman problem. The traveling salesman problem is a NP-hard (read: very hard) problem in computer science; The problem involves finding the shortest possible route between cities, visiting each city only once. ‘Traveling salesman problems’ are notorious for keeping supercomputers busy for days. NP-hard problem – Examples Excerpt: Another example of an NP-hard problem is the optimization problem of finding the least-cost cyclic route through all nodes of a weighted graph. This is commonly known as the traveling salesman problem. http://en.wikipedia.org/wiki/NP-hard#Examples Finding: Bees Solve The Traveling Salesman Problem – October 2010 Excerpt: It is a classic problem in the field of computer science: In what order should a salesman visit his prospects? The traveling salesman problem may appear simple but it has engaged some of the greatest mathematical minds and today engages some of the fastest computers. This makes new findings, that bees routinely solve the problem before pollinating flowers, all the more remarkable. https://uncommondescent.com/intelligent-design/finding-bees-solve-the-traveling-salesman-problem/ What is interesting is that quantum computers excel in exactly this ‘narrow’ area of computation: The Limits of Quantum Computers – March 2008 Excerpt: “Quantum computers would be exceptionally fast at a few specific tasks, but it appears that for most problems they would outclass today’s computers only modestly. This realization may lead to a new fundamental physical principle” http://www.scientificamerican.com/article.cfm?id=the-limits-of-quantum-computers Speed Test of Quantum Versus Conventional Computing: Quantum Computer Wins – May 8, 2013 Excerpt: quantum computing is, “in some cases, really, really fast.” McGeoch says the calculations the D-Wave excels at involve a specific combinatorial optimization problem, comparable in difficulty to the more famous “travelling salesperson” problem that’s been a foundation of theoretical computing for decades.,,, “This type of computer is not intended for surfing the internet, but it does solve this narrow but important type of problem really, really fast,” McGeoch says. http://www.sciencedaily.com/releases/2013/05/130508122828.htm Since it is obvious that there is not a ‘classical’ supercomputer in the DNA, or cell, busily computing answers to this monster traveling salesman problem, in a purely ‘material’ fashion, by crunching bits, then it is readily apparent that this monster ‘traveling salesman problem’, for DNA repair, is somehow being computed by ‘non-local’ quantum computation within the cell and/or within DNA; Quantum Entanglement/Information in DNA – video https://vimeo.com/92405752 Is DNA a quantum computer? Stuart Hameroff Excerpt: DNA could function as a quantum computers with superpositions of base pair dipoles acting as qubits. Entanglement among the qubits, necessary in quantum computation is accounted for through quantum coherence in the pi stack where the quantum information is shared,,, http://www.quantumconsciousness.org/dnaquantumcomputer1.htm The trouble for Darwinists with the finding of quantum entanglement/information, and computation, in DNA is that quantum entanglement/information requires a non-local, beyond space and time, cause in order to explain its effect. Looking beyond space and time to cope with quantum theory – 29 October 2012 Excerpt: “Our result gives weight to the idea that quantum correlations somehow arise from outside spacetime, in the sense that no story in space and time can describe them,” http://www.quantumlah.org/highlight/121029_hidden_influences.php Yet neo-Darwinism holds that information ‘emerges’ from within space-time particles. Scientifically, finding quantum entanglement/information in molecular biology is a direct empirical falsification of a primary Darwinian precept! Another place that a NP complete problem is found in molecular biology is in protein folding: Combinatorial Algorithms for Protein Folding in Lattice Models: A Survey of Mathematical Results – 2009 Excerpt: Protein Folding: Computational Complexity 4.1 NP-completeness: from 10^300 to 2 Amino Acid Types 4.2 NP-completeness: Protein Folding in Ad-Hoc Models 4.3 NP-completeness: Protein Folding in the HP-Model http://www.cs.brown.edu/~sorin/pdfs/pfoldingsurvey.pdfbornagain77
June 11, 2014
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Is DNA the most efficient information storage device known to man, vastly exceeding what man has ever done in computers? Yes! Has ID given a experimental account for the origin of that astonishing DNA molecule? God did it Has ID given a empirical account for the origin of digital information within DNA? God did it Is ID given a free ride in theology??? You bet your life!Acartia_bogart
June 11, 2014
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I'm also not sure why you think the 98% comparison wouldn't include ORFans (of which there are very few in humans..)wd400
June 11, 2014
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JDD, You've spent an awful lot of time and words trying to find a awy in which Tomkins results can stand up for someone with no emotional investment. I don't mean to suggest you are conviously biased toward creationist literature, just that you should check your unconcious bias
I claimed to not be an expert in BLASTN algorithm parameters. I am a cell biologist and I claim to have a level of education (from one of the top universities in my country, with one of the top graduating grades for undergrad and multiple first author publications from my PhD and post-docs, thus not just someone who has “done a degree”) that allows me to understand data. I am not an expert, but I have a decent chance of being able to grasp scientific data due to my background. However I admit I am not an expert in that field and in particular, in that methodology.
Well, you haven't grapsed this data or even the meaning of the ungaped flag, so I'm not sure why you career to date is of any relevance.
I am not ignoring other studies, you miss the point here. The point is that this appeared to be an optimised sequence alignment that does not just rely on small parts of the chromosome but slices it up. I am interested in the whole chromosome regardless ofwhat you think is worth aligning or not (protein coding or not),
Then you are defiately ignoring previous work, as previous work focuses on whole chromosomes not just protein coding (or even annotated) regions.
But of course you would never accept anything from such publications anyway – as you say, you have predetermined that anything in there must be pseudoscience and it is a pseudojournal. You have already taken that stance.
It was you who claimed to was reasoanable to assume something was well done since it was in a journal. I meerly pointed out that it wasn't a real journal. I have explicitly said many times in this thread why Tomkins results are not as people claim they are, those are the reasons I dismiss them (not the venue they appeared in).wd400
June 11, 2014
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Is DNA the most efficient information storage device known to man, vastly exceeding what man has ever done in computers? Yes! Has Darwinism given a experimental account for the origin of that astonishing DNA molecule? Not even close! Has Darwinism given a empirical account for the origin of digital information within DNA? Not even close! Is Darwinism given a free ride in science?? You bet your life! notes: Information Storage in DNA by Wyss Institute - video https://vimeo.com/47615970 Quote from preceding video: "The theoretical (information) density of DNA is you could store the total world information, which is 1.8 zetabytes, at least in 2011, in about 4 grams of DNA." Sriram Kosuri PhD. - Wyss Institute Storing information in DNA - Test-tube data - Jan 26th 2013 Excerpt: Dr Goldman’s new scheme is significant in several ways. He and his team have managed to set a record (739.3 kilobytes) for the amount of unique information encoded. But it has been designed to do far more than that. It should, think the researchers, be easily capable of swallowing the roughly 3 zettabytes (a zettabyte is one billion trillion or 10²¹ bytes) of digital data thought presently to exist in the world and still have room for plenty more. http://www.economist.com/news/science-and-technology/21570671-archives-could-last-thousands-years-when-stored-dna-instead-magnetic ,,, If we were dealing with a real science instead of a 'religion' then, since Darwinism has not explained even the first steps, then it certainly would not be given a free pass on any of its other claims. But alas we are not dealing with a real science!bornagain77
June 11, 2014
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Thanks for the links BA77 and reference, much appreciated. Acartia - this is my whole point of this whole discussion, down to what you have said. See you are still saying 98% similarity but that is misleading. That does not take into account indels and ORFans. Even L Moran accepts that: http://sandwalk.blogspot.co.uk/2012/01/whats-difference-between-human-and.html Then he claims that most of the differences are in the 90% junk, but does not reference this, as far as I can see, in papers modern enough to take into account that at least now we know a bit more of the genome is functional that we first thought. Plus, when you read this you see many assumptions are heavily laden within such writings. For example:
These genes are members of gene families and all that's happened is that 689 orthologous genes have [either arisen by duplication in the human lineage or] been lost by deletion in the chimp lineage or 689 new parologous genes have been "born" by gene duplication (or some combination).
How do you know this? These are largely assumptions. Because they are in a gene family they MUST have duplicated or been lost. For some, there may be some supportive "evidence" of bits of one gene looking like bits of another existing one but again, this is pure assumption. Additionally, Moran puts a heavy emphasis a few times on the likelihood of sequencing errors tidying up many of the differences. That argument could work the other way around and even more so when parts have been put together of the chimp chromosome based on a human template. The point is what willh alludes to, and is the same reason why if 90% of the genome is not junk, but say only 50% is, it creates a much larger problem to explain in evolutionary terms. To me, the more we find out the more it is heading in that direction. However to say we are 98.5% similar to chimps, to still teach that in the classroom is bogus and not true. The ONLY reason that "fact" is still taught to people is because it supports the evolutionary framework. You can guarantee if it was 94% in the first instance then they found out it was actually 98.5% what was taught would be rapidly changed! But of course no, there is no bias in evolutionary biology.Dr JDD
June 11, 2014
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wd400 wrote: "Willh, ungapped means what I’ve said it means. You are welcome to download the BLAST executables and test it for yourself." Ok, fair comment. Though I am hoping to gain a bit more insight into how the BLAST programs actually work, at-least before any attempt to even use them. For instance how the initial string of 11 letter words are generated from the query set (chimp DNA?), then compared to the base (human DNA?), expanded, and finally scored. Are those comparisons always directly compared crosswise for instance, or are they shifted along to generate a high scoring match?willh
June 11, 2014
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Acartia_bogart wrote: "The logical conclusion would be that chimps are still the closest relative to humans. So, nothing has changed." Respectfully there is a difference, as 28% more changes in a 3.1 billion or more nucleotide long genome, requires much more work ... be it by random variations plus natural selection, or by design.willh
June 11, 2014
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If I have been following the discussion properly, there is a disagreement between the genetic similarity between chimps and humans. The discrepancy is between comparisons performed using well thought out, rational and accepted practices (as represented by Piotr, WD400 and numerous peer reviewed papers) and one comparison performed by Tomkins, using a procedure that has been soundly criticized for its inappropriateness (as represented by BA77 and others, using creationist blogs, utube posts and other questionable sources). But, for the sake of argument, let's assume that Tomkins approach is valid and the % similarity between chimps and humans is less that the 98% that was previously thought. It is reasonable to assume that comparisons between the genetics of other species would suffer the same fate (i.e., lower the % similarity numbers between any two species that was previously looked at). The logical conclusion would be that chimps are still the closest relative to humans. So, nothing has changed.Acartia_bogart
June 11, 2014
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Dr JDD, I'm sure if you have any specific questions, Dr. Tomkins will be gracious enough to answer any concerns you have in detail so that you can be assured that his research is done with integrity. His contact info can be found here: http://creationwiki.org/Jeffrey_Tomkins as well, Here is a recent book of his (2012) that you may find insightful: More Than a Monkey: The Human-Chimp DNA Similarity Myth http://creationwiki.org/More_Than_a_Monkey:_The_Human-Chimp_DNA_Similarity_Mythbornagain77
June 11, 2014
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wd400 @202 I am not bending over backwards. Who is selectively reading now? I said I would not use this paper in arguments to support ID etc, as it is not clear to me the results are valid. I think that is being quite scientific and fair. I claimed to not be an expert in BLASTN algorithm parameters. I am a cell biologist and I claim to have a level of education (from one of the top universities in my country, with one of the top graduating grades for undergrad and multiple first author publications from my PhD and post-docs, thus not just someone who has "done a degree") that allows me to understand data. I am not an expert, but I have a decent chance of being able to grasp scientific data due to my background. However I admit I am not an expert in that field and in particular, in that methodology. If you have never done mass spec analysis you cannot claim to be an expert in that method but if someone reports a finding you can use your scientific knowledge to make judgements on their interpretation as long as it does not require extensive knowledge about the technique. We all as scientists must do that otherwise we are 100% at the mercy of an "expert". We have to rely on methodology done in a proper manner, as reported, to an appropriate level as you would expect an expert to do. I do not/did not know you are an "expert" in BLAST alignments and algorithm codes for these alignments. I also was trying to understand what -ungapped actually meant. You are just a person on the internet, not a name whom I can check qualifications. Therefore a good scientist would try to establish what the method truly means based on what is reported, which is what I have said I am trying to do. I have also emphasised and made it clear Iwould not personally use that publication as support for any view unless I could be very confident that the methodology did not do as you state it does. I am not ignoring other studies, you miss the point here. The point is that this appeared to be an optimised sequence alignment that does not just rely on small parts of the chromosome but slices it up. I am interested in the whole chromosome regardless ofwhat you think is worth aligning or not (protein coding or not), I am interested in the whole thing as I do not personally subscribe to the idea that >95% of it is junk. That is not me "not listening to the experts" that is me reserving judgement on something that has only anecdotally been shown and is a huge assumption that was wrong 15 years ago, so what we still don't know is probably wrong to assume today too. PaV has also raised some interesting points but your behavious is quite common in any interactions I seem to have with naturalist evolutionists over this subject. If I concede something that could support them they either miss the fact that I am being fair, over-emphasise it, or pronounce victory as I have conceded a point. Yet the vast majority of evolutionists never will concede anything because they could not possibly agree with anything an IDer said. As per here, you are still saying I am bending over backwards to support the paper yet I am certainly not. It is quite bizzare to me that you would make this statement after I have clearly said I would not hold to those findings as accurate until I could definitively establish what those paramters mean. But of course you would never accept anything from such publications anyway - as you say, you have predetermined that anything in there must be pseudoscience and it is a pseudojournal. You have already taken that stance. Well I can assure you plenty of faked results and plenty of false data has appeared in the most prestigious journals around (Nature, Science, etc). Yet that does not make them pseudojournals or any less authoritative journals to pulish scientific findings in. I try to take each publication as it is, and assess the quality and likely interpretations from the data. When I see a publication that shows soft-body preservation from 100s of millions of years ago, embryos still intact, when I see plant analysis from 100s of MYA with no change in evolution from then and now, when I see a vast number of incredibly complex mechanisms for controling gene regulation and protein expression that makes us who we are and not chimps or another mammal, my logic does not automatically go "wow evolution is so clever!" It says, "well this does not fit with the mechanisms proposed of evolution and does not make sense to arise naturally." Yet any publication that comes out with novel complexities simply tags on the end "Evolution is more complex than we though" or "evolution can acheive more than we thought" yet WE who doubt that are the intellectually challenged ones operating in pseudoscience? Please, come on now. That is not science.Dr JDD
June 11, 2014
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Question, How many incongruences in data and theory can you find in these two papers? Recent Genetic Research Shows Chimps More Distant From Humans,,, – Jan. 2010 Excerpt: A Nature paper from January, 2010 titled, “Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content,” found that Y chromosomes in humans and chimps “differ radically in sequence structure and gene content,” showing “extraordinary divergence” where “wholesale renovation is the paramount theme.”,,, “Even more striking than the gene loss is the rearrangement of large portions of the chromosome. More than 30% of the chimp Y chromosome lacks an alignable counterpart on the human Y chromosome, and vice versa,,,” http://www.evolutionnews.org/2010/04/recent_genetic_research_shows.html The chimpanzee MSY contains twice as many massive palindromes as the human MSY, yet it has lost large fractions of the MSY protein-coding genes and gene families present in the last common ancestor. http://www.nature.com/nature/journal/v463/n7280/full/nature08700.html Theory of the ‘Rotting’ Y Chromosome Dealt a Fatal Blow – February 2012 Excerpt: “the sequence of the rhesus Y, shows the chromosome hasn’t lost a single ancestral gene in the past 25 million years. By comparison, the human Y has lost just one ancestral gene in that period, and that loss occurred in a segment that comprises just 3% of the entire chromosome”, “,,,earlier work comparing the human and chimpanzee Ys revealed a stable human Y for at least six million years. “Now our empirical data fly in the face of the other theories out there. With no loss of genes on the rhesus Y and one gene lost on the human Y, it’s clear the Y isn’t going anywhere.” http://www.sciencedaily.com/releases/2012/02/120222154359.htmbornagain77
June 10, 2014
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That's not the way I read it at all. Moreover, You claim DNA can 'evolve' quickly? Really? Where is your proof? The Paradox of the "Ancient" (250 Million Year Old) Bacterium Which Contains "Modern" Protein-Coding Genes: “Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.” Heather Maughan*, C. William Birky Jr., Wayne L. Nicholson, William D. Rosenzweig§ and Russell H. Vreeland ; http://mbe.oxfordjournals.org/cgi/content/full/19/9/1637 Geobiologist Noffke Reports Signs of Life that Are 3.48 Billion Years Old - 11/11/13 Excerpt: the mats woven of tiny microbes we see today covering tidal flats were also present as life was beginning on Earth. The mats, which are colonies of cyanobacteria, can cause unusual textures and formations in the sand beneath them. Noffke has identified 17 main groups of such textures caused by present-day microbial mats, and has found corresponding structures in geological formations dating back through the ages. http://www.odu.edu/about/odu-publications/insideodu/2013/11/11/topstory1 Scientists find signs of life in Australia dating back 3.48 billion years - Thu November 14, 2013 Excerpt: “We conclude that the MISS in the Dresser Formation record a complex microbial ecosystem, hitherto unknown, and represent one of the most ancient signs of life on Earth.”... “this MISS displays the same associations that are known from modern as well as fossil” finds. The MISS also shows microbes that act like “modern cyanobacteria,” http://www.cnn.com/2013/11/13/world/asia/australia-ancient-life/ Static evolution: is pond scum the same now as billions of years ago? Excerpt: But what intrigues (paleo-biologist) J. William Schopf most is lack of change. Schopf was struck 30 years ago by the apparent similarities between some 1-billion-year-old fossils of blue-green bacteria and their modern microbial counterparts. "They surprisingly looked exactly like modern species," Schopf recalls. Now, after comparing data from throughout the world, Schopf and others have concluded that modern pond scum differs little from the ancient blue-greens. "This similarity in morphology is widespread among fossils of [varying] times," says Schopf. As evidence, he cites the 3,000 such fossils found; http://www.thefreelibrary.com/Static+evolution%3A+is+pond+scum+the+same+now+as+billions+of+years+ago%3F-a014909330 Some theory you got there wd400, it explain both billions of years of stasis and 6 million years of wholesale remodeling of the Y chromosome. Shoot, your theory is so great News referenced a story where they are now trying to explain the origin of the universe with it. I'm thinking of hiring Darwinism to build me a house. There is simply nothing it can't do! :)bornagain77
June 10, 2014
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BA and Querius Do you even read these things? The paper from 1995 (!) found k no variants in one 700 bp intron the other paper is about turnover in gene number not divergence homologous sequences. They don't establish that the Y is evolving anything other than quickly.wd400
June 10, 2014
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wd400, I find it interesting that you, a Neo-Darwinist, would have the audacity to call anything 'pseudo', since the plain fact of the matter is that Darwinism itself is the reigning king of pseudo-sciences. In fact it is anti-science! Even now, you offer no empirical proof that transformation of form is possible, you simply assume it to be true and never shoulder any real burden of proof! "nobody to date has yet found a demarcation criterion according to which Darwin(ism) can be described as scientific" - Imre Lakatos (November 9, 1922 – February 2, 1974) a philosopher of mathematics and science, quote was as stated in 1973 LSE Scientific Method Lecture Is evolution pseudoscience? Excerpt:,,, Thus, of the ten characteristics of pseudoscience listed in the Skeptic’s Dictionary, evolution meets nine. Few other pseudosciences - astrology, astral projection, alien abduction, crystal power, or whatever — would meet so many. http://creation.com/is-evolution-pseudoscience Darwinian Evolution is a Pseudo-Science - Part II https://docs.google.com/document/d/1oaPcK-KCppBztIJmXUBXTvZTZ5lHV4Qg_pnzmvVL2Qw/editbornagain77
June 10, 2014
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Pav, That reference doesn't refer to the same methods (or data) as the one under discussion, so it's not possible to compare the result of gapped and ungapped alignments. Of course, it would be very easy to do that. I wonder why Tomkins didn't?wd400
June 10, 2014
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Willh, ungapped means what I've said it means. You are welcome to download the BLAST executables and test it for yourself.wd400
June 10, 2014
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JDD, Here's the situation. We are talking about a topic you admit to having no expert knowledge in. There is a paper in a YEC pseudo-journal claiming 70% identity between human and chimps. Every other paper (including the chimp genome paper) finds ~98% in SNPs, a bit less including indels. The Y-chrom papers can't be support for the 70% finding because the paper in the YEC-pseudo journal does not find 70% identity between Y chromosomes. The YEC pseudo-journal paper uses a setting that someone who does know the first thing about sequence analysis has told you will behave very strangely, and I've asked you to check that yourself. In the fact of all of that you are leaning over backwards to finding a reading of the paper that supports Tomkins result. Why are you so credulous about the Tomkins result but so skeptical about the findings of mainstream science?wd400
June 10, 2014
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bornagain77 quoted
Theory of the ‘Rotting’ Y Chromosome Dealt a Fatal Blow – February 2012 Excerpt: “the sequence of the rhesus Y, shows the chromosome hasn’t lost a single ancestral gene in the past 25 million years.
Not a problem for the TOE! It simply shows that there obviously "musta" been little or no selection pressure on the rhesus Y chromosome in the past 25 million years. LOL The theory of evolution can explain anything, but successfully predicts nothing. -QQuerius
June 10, 2014
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REC claims, "rapidly evolving region like the Y (chromosome)" yet, CHROMOSOME STUDY STUNS EVOLUTIONISTS Excerpt: To their great surprise, Dorit and his associates found no nucleotide differences at all in the non-recombinant part of the Y chromosomes of the 38 men. This non-variation suggests no evolution has occurred in male ancestry. http://www.reasons.org/interpreting-genesis/adam-and-eve/chromosome-study-stuns-evolutionists Theory of the 'Rotting' Y Chromosome Dealt a Fatal Blow - February 2012 Excerpt: "the sequence of the rhesus Y, shows the chromosome hasn't lost a single ancestral gene in the past 25 million years. By comparison, the human Y has lost just one ancestral gene in that period, and that loss occurred in a segment that comprises just 3% of the entire chromosome", ",,,earlier work comparing the human and chimpanzee Ys revealed a stable human Y for at least six million years. "Now our empirical data fly in the face of the other theories out there. With no loss of genes on the rhesus Y and one gene lost on the human Y, it's clear the Y isn't going anywhere." http://www.sciencedaily.com/releases/2012/02/120222154359.htm HMMM???bornagain77
June 10, 2014
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Edit: Found another example where the gap score was tallied separately from the match / mismatch score ... again I stress: I think?!willh
June 10, 2014
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"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." Ok, from someone who hasn't ever seen the BLASTN search tool or the inside of a lab even, I'll throw this in at any rate. When I do a 'search' for BLASTN terminology definitions, I get a description of gapped and ungapped as settings that count, or don't count, toward a certain score. An example comparing two sequences, a matching nucleotide pair score a +1, a miss match -2. Gap scoring it seems can be arbitrarily set for a value at each occurrence and for length, or set to not score at all ... err as I say it would seem. The score is a number that doesn't appear to relate to a percentage in the illustrations used. And as a by the way comment I ran across this statement: "there is no widely accepted theory for selecting gap costs. Whatever is going on, the setting of 'ungapped' may not be causing the effect we are debating over; it may not be causing the dramatic percentage interpretations we seem to fear.willh
June 10, 2014
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So we have an AIG author that developed a method using "optimized sequence slices" that comes up with absolute values of human chimp identity lower than a standard sequence alignment. I think, given what the technique does, it is pretty clear why, and also that this is a bit silly. But what does this few percent he fights for with this odd tactic buy you? What I'd like to see is you, or the author, apply this method to other genomes, and list the distances. Bet it looks like a pretty standard phylogeny. Please. Go right ahead. You have the resources. Also, apply it to human genomes as a reference point. How identical to each other are we with the metric? Evolutionary biology doesn't rely on cats and dogs or worms and us being a certain predicted % identical to establish phylogeny. You can toss in additional criteria (remember the hilarious 30bp search window promoted here!), and skew the numbers down, but the trend will persist. Other than making some AIG "we aren't THAT related" talking point, who cares? Even for humans and chimps, in a rapidly evolving region like the Y, we see less conservations with chimps. But we'd predict more conservation than in gorillas, monkeys, mice, etc.REC
June 10, 2014
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@PaV: "This is the ‘other side’ of what’s going on. Are you willing to accept that perhaps evolutionists have ‘fudged’ the data?" I have not read these papers so I am not qualified to comment on their veracity. I will leave that to WD400 as he is obviously well versed on the subject. However, if, in the papers, they describe how they screen/filter the data then they are not fudging anything. People reading the papers, including the peer reviewers, are free to question the methodology and rebut the work in subsequent papers.Acartia_bogart
June 10, 2014
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