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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
wd400 and ABogart: From Tomkins' 2011c paper's introduction:
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, ?ltering and selection before being aligned, summarized, and discussed. Non-alignable regions are typically omitted and gaps in alignments are often discarded or obfuscated.
This is the 'other side' of what's going on. Are you willing to accept that perhaps evolutionists have 'fudged' the data?PaV
June 10, 2014
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wd400: I recommend that you look at Tables 1 and 2 in Tomkins' 2011c paper: From that paper:
An attempt was made to repeat a smaller subset of Wood’s research using the standard default parameters for BLASTN (word size = 11, default gapping, and an e-value = 10) and only a maximum DNA identity between chimp and human of 89% was obtained (Tomkins 2011d). This 236 J. P. Tomkins value con?icts with the reported 98+% similarity given in the Wood (2011) abstract. These preliminary results reported by both Wood and Tomkins clearly show that additional research in this area using a broader range of more carefully controlled BLASTN algorithm variables is warranted.
PaV
June 10, 2014
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Wd400:
JDD, don’t take it from me. Download the BLAST executables and compare the two sequences I posted with and without the ungapped flag. You will see I am right. I don’t why you keep on going on about the Y chromosome. As I have said it behaves different from the others, including in Tomkins analysis which does not find 70% similarity for the Y. Tomkins numbers don’t agree with any published results in real journals. I really find it bizare that you and other evolution “skeptics” would go to such lengths to protect a study with a conclusion you’d like to be true.
I will when I have had time to download the program and try to replicate this but I am not an expert in that area and using that, thus do not want to wholly rely on my own inabilities to give the answer to the question I am asking. It would be easiest if Tomkins could directly address the question simply – if there is an indel, does that throw the alignment off giving a lower similarity than actually is there, like your example above. I think your final paragraph is a bit unfair and assumptive. I am trying to establish what the exact methodology was around this issues with a shifting of the code due to indel and how that alters (if it does) the alignment. This is a scientific publication. Initially from what was said, it seemed like Tomkins went about a very conservative approach and also claimed to take into account gaps, thus I could not easily decipher from his publication any reason to assume that your example would in fact be counted the way you claim. This was compounded by the fact that when I tried to determine exactly what “-ungapped” codes for (as linked above) it appeared to me to remove pre-annotated “-“ gaps, but as I conceded, I may be wrong. I would like to take most scientific publications at face value, with regards to scientific methodology although it is worth questioning the method. Where I know little about some method though, I am at the mercy of the person who is meant to be the expert in that method. Where I usually disagree is in the interpretation of results and I believe many IDers are the same with evolutionary publications. So where am I going to such lengths to protect this study? I think I have shown a clear desire to interpret the data correctly, and initially err on the side that the expert (Tomkins is an established geneticist who published many papers in the “secular” research world) knows what they are doing in terms of methodology. I have tried to interrogate the paper on those grounds. I am not going out of my way to try and protect anything. I personally will happily concede that the findings are flawed if indeed it can be shown that Tomkins used the approach you state he has used, i.e. an insertion of a base 2/3 of the way down a stretch of DNA would take the alignment to 66% similar, a conclusion I disagree with. IF that is how this study was done, then yes I would personally not defend it nor use it as “proof” that chimps and humans are really only 70% similar at best. And the reason I am apparently “obsessed” with the Y chromosome is that it is the only recent paper with a decent copy of the chimp Y chromosome that has gone to such depths to compare with the human one – that is the only reason I regularly quote it. That is not an agenda of mine, it is simply because I cannot find other recent publications that compare in that detail individual chromosomes beyond the gene-coding regions, as we now know that a fair amount of the genome is active and potentially has function, I am interested in the differences between all of the DNA, not just protein coding. I am interested in pseudogenes, in ORFans, in indels (many have function), in other non-coding areas of the genome. Clearly humans and chimps are very different so I am interested in where this comes from. If something is shown to be a bad study I will not personally use it as proof for my worldview. So please do not assume that, as nowhere have I gone to extraordinary lengths to defend something that is “obviously” wrong – my point is this is NOT obviously wrong. It may be wrong and you have provided an argument for that, which I am certainly trying to confirm and understand better. For now though, this [70% homology] is not something I would personally use in my defence of an ID view. However the point remains – I (or anyone) don’t need this paper to be true to defend ID. If it was true, it would be quite strong evidence against common descent 6-7mya from chimps. However, that does not hinge on whether this is true or not. Much like what PaV alludes to above, there are numerous other studies not to mention mathematical models that point to the flaws of UCD and naturalistic evolution in the time-frame given to generate such believable attribution to the proposed theory and mechanisms. The emergence of epigenetics, the ENCODE data, the day-by-day increase in the apparent complexity of the genome especially with non-coding regions playing important functional roles, all of these things (to just name a mere handful) remain and they certainly are not “clutching at straws” – they are genuine issues that evolution fails to address, explain, or accommodate.Dr JDD
June 10, 2014
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@WD400: "I really find it bizare that you and other evolution “skeptics” would go to such lengths to protect a study with a conclusion you’d like to be true. Do you really have to ask? Do "straws" and "clutching" come to mind?Acartia_bogart
June 10, 2014
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Moreover, there is good reason to believe that hidden, and unproven, assumptions lie at the base of many of the algorithms making genetic comparisons:
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 “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 (15:25 minute mark) http://intelligentdesign.podomatic.com/entry/2014-05-30T17_33_15-07_00 Contradictory Trees: Evolution Goes 0 For 1,070 - Whif Excerpt: One of evolution’s trade secrets is its prefiltering of data to make it look good, but now evolutionists are resorting to postfiltering of the data as well.,,, Prefiltering is often thought of merely as cleaning up the data. But prefiltering is more than that, for built-in to the prefiltering steps is the theory of evolution. Prefiltering massages the data to favor the theory. The data are, as philosophers explain, theory-laden. But even prefiltering cannot always help the theory.,,, http://darwins-god.blogspot.com/2013/06/contradictory-trees-evolution-goes-0.html
As well, contrary to what wd400 would prefer to believe, and in spite of these biased algorithms, the overall genetic tree of life is turning out to be as much, if not more, of a problem for Darwinists as the fossil record has turned out to be:
Logged Out - Scientists Can't Find Darwin's "Tree of Life" Anywhere in Nature by Casey Luskin - Winter 2013 Excerpt: the (fossil) record shows that major groups of animals appeared abruptly, without direct evolutionary precursors. Because biogeography and fossils have failed to bolster common descent, many evolutionary scientists have turned to molecules—the nucleotide and amino acid sequences of genes and proteins—to establish a phylogenetic tree of life showing the evolutionary relationships between all living organisms.,,, Many papers have noted the prevalence of contradictory molecule-based phylogenetic trees. For instance: • A 1998 paper in Genome Research observed that "different proteins generate different phylogenetic tree[s]."6 • A 2009 paper in Trends in Ecology and Evolution acknowledged that "evolutionary trees from different genes often have conflicting branching patterns."7 • A 2013 paper in Trends in Genetics reported that "the more we learn about genomes the less tree-like we find their evolutionary history to be."8 Perhaps the most candid discussion of the problem came in a 2009 review article in New Scientist titled "Why Darwin Was Wrong about the Tree of Life."9 The author quoted researcher Eric Bapteste explaining that "the holy grail was to build a tree of life," but "today that project lies in tatters, torn to pieces by an onslaught of negative evidence." According to the article, "many biologists now argue that the tree concept is obsolete and needs to be discarded.",,, Syvanen succinctly summarized the problem: "We've just annihilated the tree of life. It's not a tree any more, it's a different topology entirely. What would Darwin have made of that?" ,,, "battles between molecules and morphology are being fought across the entire tree of life," leaving readers with a stark assessment: "Evolutionary trees constructed by studying biological molecules often don't resemble those drawn up from morphology."10,,, A 2012 paper noted that "phylogenetic conflict is common, and [is] frequently the norm rather than the exception," since "incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species."12,,, http://www.salvomag.com/new/articles/salvo27/logged-out.php Richard Dawkins: How Could Anyone “Possibly Doubt the Fact of Evolution” - Cornelius Hunter - February 27, 2014 Excerpt: there is “no known mechanism or function that would account for this level of conservation at the observed evolutionary distances.”,,, the many examples of nearly identical molecular sequences of totally unrelated animals are “astonishing.”,,, “data are routinely filtered in order to satisfy stringent criteria so as to eliminate the possibility of incongruence.”,,, he has not found “a single example that would support the traditional tree.” It is, another evolutionist admitted, “a very serious incongruence.” “the more molecular data is analysed, the more difficult it is to interpret straightforwardly the evolutionary histories of those molecules.” And yet in public presentations of their theory, evolutionists present a very different story. As Dawkins explained, gene comparisons “fall in a perfect hierarchy, a perfect family tree.” This statement is so false it isn’t even wrong—it is absurd. And then Dawkins chastises anyone who “could possibly doubt the fact of evolution.” Unfortunately this sentiment is typical. Evolutionists have no credibility. http://darwins-god.blogspot.com/2014/02/richard-dawkins-how-could-anyone.html
Thus wd400's reliance on genetic similarity in order to make his case for Darwinian evolution is not nearly as robust as he imagines it to be. Moreover, the trend in evidence with RNA's is even worse than the DNA comparisons were for Darwinists:
Phylogeny: Rewriting evolution - Tiny molecules called microRNAs are tearing apart traditional ideas about the animal family tree. - Elie Dolgin - 27 June 2012 Excerpt: “I've looked at thousands of microRNA genes, and I can't find a single example that would support the traditional tree,” he says. "...they give a totally different tree from what everyone else wants.” (Phylogeny: Rewriting evolution, Nature 486,460–462, 28 June 2012) (molecular palaeobiologist - Kevin Peterson) Mark Springer, (a molecular phylogeneticist working in DNA states),,, “There have to be other explanations,” he says. Peterson and his team are now going back to mammalian genomes to investigate why DNA and microRNAs give such different evolutionary trajectories. “What we know at this stage is that we do have a very serious incongruence,” says Davide Pisani, a phylogeneticist at the National University of Ireland in Maynooth, who is collaborating on the project. “It looks like either the mammal microRNAs evolved in a totally different way or the traditional topology is wrong. http://www.nature.com/news/phylogeny-rewriting-evolution-1.10885
Thus, when taking the whole body of knowledge into consideration, there is very good reason to doubt that wd400 is being forthright with us with Tomkins current 70% study.,,, Hopefully this inability for wd400 to face the overall evidence soberly and honestly, and admit that his case is weak because of that overall body of evidence, to put it kindly, will change. But, I hold little hope that he will change. Sad!bornagain77
June 10, 2014
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"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" - Tomkinsbornagain77
June 10, 2014
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JDD, don't take it from me. Download the BLAST executables and compare the two sequences I posted with and without the ungapped flag. You will see I am right. I don't why you keep on going on about the Y chromosome. As I have said it behaves different from the others, including in Tomkins analysis which does not find 70% similarity for the Y. Tomkins numbers don't agree with any published results in real journals. I really find it bizare that you and other evolution "skeptics" would go to such lengths to protect a study with a conclusion you'd like to be true.wd400
June 10, 2014
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Hi wd400, I suspected that this is where you were getting the “not taking into account gaps” from: the use of “-ungapped” in that materials in methods. However, the reason I probed is because I am honestly unsure of what this refers to and cannot make the inference that it simply does not take into account gaps at all. That is one scenario, but based on the language throughout the publication about the most optimal sequence alignment, that is the most conservative, I find it odd if this was the case. However I am not a programmer, although I regularly use the BLAST programs (but rarely BLASTN, usually BLASTP) and always use the GUI selections provided with the online query forms. However, I did come across this: http://biopython.org/DIST/docs/api/Bio.Seq.Seq-class.html#ungap Perhaps someone with more computer knowledge than me can try to interpret what this means. To my simple mind, it appears that the “ungap” could refer to removing any gaps in the original sequence (i.e. any unannotated sequence, such as “-“ as opposed to not allowing gaps in the alignment). It would be most useful if someone like Tomkins who regularly uses the scripts for performing BLAST analyses could in fact confirm what “-ungapped” actually does in this context. I.e. if it does not take into account gaps in an alignment (so just performs a very rigid best fit alignment), or removes annotated gaps prior to any alignment, or, something else I have not considered here. I cannot make the assumption one way or another that “-ungapped” refers to a very specific alignment tool as it would be purely an assumption of speculation. As per the points above, I would expect the alignments to be even lower if the analysis was done as per your original suggestion, and, in particular the fact that this seems to agree with other published work for example the detailed look at the MSY chromosome.Dr JDD
June 10, 2014
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Dr JDD, Thanks so much for taking the time to explain Dr Thomkins' conservative methodology! And also for confirming that the 98.5% figure is cherry-picked, and the larger genome in humans seems to be either ignored, or explained away as evolutionary divergence without even the slightest twinge of concern that the chimpanzee genome should also have been similarly diverging during that time, perhaps keeping pace with the human genome. But as has become ever clearer, The theory of evolution can explain anything, but successfully predicts nothing. In other words, if the chimpanzee genome were discovered to be 10-12% larger than the human genome, this would also be effortlessly "explained" somehow. As it's becoming increasingly apparent to all but the most ideologically contaminated, a theory that's infinitely malleable is utterly useless. -QQuerius
June 9, 2014
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Acartia_bogart, remember this: https://uncommondescent.com/intelligent-design/does-consciousness-not-involve-quantum-principles/#comment-502351 You said such and such would falsify Darwinism. When I showed that, using your own criteria, Darwinism was falsified, you refused to acknowledge it! Yet despite this cowardly act on your part, you go on to hypocritically state this: "You wouldn’t accept empirical evidence (and there is a lot) even if it is presented." To which I say, Yes I would. No there isn't any. It has never been presented.,,, One molecular machine, such as the Bacterial Flagellum, arising by unguided processes would fit the bill quite well. As to eyewitness evidence for God creating, what do you think of the whole Cosmic Background radiation thing? Two Nobel Laureates who discovered it consider it quite convincing: The best data we have [concerning the Big Bang] are exactly what I would have predicted, had I nothing to go on but the five books of Moses, the Psalms, the bible as a whole. Dr. Arno Penzias, Nobel Laureate in Physics - co-discoverer of the Cosmic Background Radiation - as stated to the New York Times on March 12, 1978 “Certainly there was something that set it all off,,, I can’t think of a better theory of the origin of the universe to match Genesis” Robert Wilson – Nobel laureate – co-discover Cosmic Background Radiation As well: “There is no doubt that a parallel exists between the big bang as an event and the Christian notion of creation from nothing.” George Smoot – Nobel laureate in 2006 for his work on COBE "Now we see how the astronomical evidence supports the biblical view of the origin of the world. The details differ, but the essential elements in the astronomical and biblical accounts of Genesis are the same: the chain of events leading to man commenced suddenly and sharply at a definite moment in time, in a flash of light and energy." Robert Jastrow – Founder of NASA’s Goddard Institute – Pg.15 ‘God and the Astronomers’ If you do not consider that positive evidence for God, there is really little I can do save to expose you for the dogmatist, instead of true seeker, that you are.bornagain77
June 9, 2014
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BA77, again, less is more. You wouldn't accept empirical evidence (and there is a lot) even if it is presented. Frankly, it is a waste of breath talking to you. Yes, I know that you will characterize it as refusing to answer the questions, but allow be to flip it back on you. What empirical evidence do you have for an intelligent designer? And I mean real evidence. Observations of an intelligent designer creating a flagellum, a water vacuole, a consciousness, a fart. I want witnesses, fossils, biochemistry. In short, the same evidence that you repeatedly demand of evolution. And see if you can do it without numerous meaningless references to creationist literature. All I am asking for is an eye witness. Because, apparently, that is all you will accept as evidence for the other side of the debate.Acartia_bogart
June 9, 2014
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wd400, does it not bother you in the least that you have no real empirical evidence supporting the feasibility of transformation of body plans, as is required in Darwinian evolution, but that you are reduced to squabbling over subjective interpretations of a misleading percentage figure??? A percentage figure that is, as Wilson and King admitted, moot to the point of explaining such radical body plan transformations as the chimp to a human in the first place??? It seems that if you were genuinely concerned with the truth of the matter, instead of just defending your preferred Darwinian worldview, then you would concede that your argument is an exercise in futility as far as true science is concerned.
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 "The closest science has come to observing and recording actual speciation in animals is the work of Theodosius Dobzhansky in Drosophilia paulistorium fruit flies. But even here, only reproductive isolation, not a new species, appeared." from page 32 "Acquiring Genomes" Lynn Margulis. The Trouble with Darwin by Kas Thomas - February 16, 2014 Excerpt: Darwin's landmark work was called The Origin of Species, yet it doesn't actually explain in detail how speciation happens (and in fact, no one has seen it happen in the laboratory, unless you want to count plant hybridization or certain breeding anomalies in fruit flies). Almost everything in evolutionary theory is based on "survival of the fittest," a tautology that explains nothing. ("Fittest" means most able to survive. Survival of the fittest means survival of those who survive.) The means by which new survival skills emerge is, at best, murky. Of course, we can't expect Darwin himself to have proposed detailed genetic or epigenetic causes for speciation, given that he was unaware of the work of Mendel, but the fact is, even today we have a hard time figuring out how things like a bacterial flagellum first appeared. When I was in school, we were taught that mutations in DNA are the driving force behind evolution, an idea that is now thoroughly discredited. The overwhelming majority of non-neutral mutations are deleterious (reducing, not increasing, survival). This is easily demonstrated in the lab. Most mutations lead to loss of function, not gain of function. Evolutionary theory, it turns out, is great at explaining things like the loss of eyesight, over time, by cave-dwelling creatures. It's terrible at explaining gain of function. It's also terrible at explaining the speed at which speciation occurs. (Of course, The Origin of Species is entirely silent on the subject of how life arose from abiotic conditions in the first place.) It doesn't explain the Cambrian Explosion, for example, or the sudden appearance of intelligence in hominids,,, http://bigthink.com/devil-in-the-data/the-trouble-with-darwin
etc.. etc.. etc..bornagain77
June 9, 2014
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I refer you to my comment #110, which quotes Tomkins 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. -ungapped.wd400
June 9, 2014
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Thank you Dr JDD for reading through Tomkins' original paper in detail and drawing out just how conservative he was in his approach. If I read what you excerpted from his paper correctly, he did not even include ORFan genes in the count. Thus when he presents his upcoming paper, if he includes ORFans (as well as dGRNs), the percentage should drop even further than the 70% figure that wd400 is currently having such a hard time accepting,
Using ENCODE Data for Human-Chimp DNA Comparisons by Jeffrey Tomkins, Ph.D.* Excerpt: In 2013, I published a research paper in which chimpanzee chromosomes were sequentially sliced into different sets of small pieces so that the algorithm could optimally compare them to human chromosomes. In so doing, I found that the chimpanzee genome was only about 70 percent similar to the human genome overall.7 More research is needed to show specifically how the new wealth of publicly available ENCODE data can be used beyond basic studies of human-chimp DNA similarity—incorporating lincRNAs and vlincRNAs to further highlight human uniqueness. Research using three large datasets produced by the ENCODE project is now underway at ICR for the purpose of addressing these questions. In a concurrent study, I am also comparing human protein-coding regions to those in chimpanzees. In combination, these new analyses will provide a much more detailed picture of what makes humans unique and will further demonstrate we are not evolved apes. http://www.icr.org/article/7856/
In congruence with all this I would like to draw out two things. First, I would like to reiterate that the anatomical differences, as Wilson and King themselves pointed out in the original 1975 paper, are far more drastic than the mythical 98.5% gene similarity number indicates. This disparity is also backed up by the fact that, anatomically speaking, humans are closer to pigs than chimps. Thus, other than rhetorical purposes for Darwinists, the mythical 98.5% figure is useless for trying to figure out what makes humans and chimps unique from each other. This was all pointed out in post 175 of the current thread:
https://uncommondescent.com/intelligent-design/a-liberating-voice-on-the-feathered-dragons/#comment-503060
The second point that I would like to draw out is something I pointed out on another thread the other day. Although Darwinists are notorious in their hubris for claiming they know for a fact how all life on earth originated, the truth is far more humbling. We are far from understanding how a organism operates in any sufficient detail, much less understanding how any organism on earth originated. Even the cellular complexity of the ‘simplest’ life on Earth has turned out to be nearly unbelievable:
To Model the Simplest Microbe in the World, You Need 128 Computers – July 2012 Excerpt: Mycoplasma genitalium has one of the smallest genomes of any free-living organism in the world, clocking in at a mere 525 genes. That’s a fraction of the size of even another bacterium like E. coli, which has 4,288 genes.,,, The bioengineers, led by Stanford’s Markus Covert, succeeded in modeling the bacterium, and published their work last week in the journal Cell. What’s fascinating is how much horsepower they needed to partially simulate this simple organism. It took a cluster of 128 computers running for 9 to 10 hours to actually generate the data on the 25 categories of molecules that are involved in the cell’s lifecycle processes.,,, ,,the depth and breadth of cellular complexity has turned out to be nearly unbelievable, and difficult to manage, even given Moore’s Law. The M. genitalium model required 28 subsystems to be individually modeled and integrated, and many critics of the work have been complaining on Twitter that’s only a fraction of what will eventually be required to consider the simulation realistic.,,, per The Atlantic
Thus researchers have not even ‘realistically’ modeled even the simplest life on Earth to the molecular level. And our ignorance at how organisms actually operate at the molecular level is orders of magnitude more acute for higher organisms than it is for the ‘simplest’ life. In fact, it is almost a guaranteed certainty that mortal man will NEVER understand how multicellular organisms operate in any meaningful detail at the molecular level:
Systems biology: Untangling the protein web – July 2009 Excerpt: Vidal thinks that technological improvements — especially in nanotechnology, to generate more data, and microscopy, to explore interaction inside cells, along with increased computer power — are required to push systems biology forward. “Combine all this and you can start to think that maybe some of the information flow can be captured,” he says. But when it comes to figuring out the best way to explore information flow in cells, Tyers jokes that it is like comparing different degrees of infinity. “The interesting point coming out of all these studies is how complex these systems are — the different feedback loops and how they cross-regulate each other and adapt to perturbations are only just becoming apparent,” he says. “The simple pathway models are a gross oversimplification of what is actually happening.” - per Nature “Complexity Brake” Defies Evolution – August 2012 Excerpt: “This is bad news. Consider a neuronal synapse — the presynaptic terminal has an estimated 1000 distinct proteins. Fully analyzing their possible interactions would take about 2000 years. Or consider the task of fully characterizing the visual cortex of the mouse — about 2 million neurons. Under the extreme assumption that the neurons in these systems can all interact with each other, analyzing the various combinations will take about 10 million years…, even though it is assumed that the underlying technology speeds up by an order of magnitude each year.”,,, Even with shortcuts like averaging, “any possible technological advance is overwhelmed by the relentless growth of interactions among all components of the system,” Koch said. “It is not feasible to understand evolved organisms by exhaustively cataloging all interactions in a comprehensive, bottom-up manner.” He described the concept of the Complexity Brake:,,, “Allen and Greaves recently introduced the metaphor of a “complexity brake” for the observation that fields as diverse as neuroscience and cancer biology have proven resistant to facile predictions about imminent practical applications. Improved technologies for observing and probing biological systems has only led to discoveries of further levels of complexity that need to be dealt with. This process has not yet run its course. We are far away from understanding cell biology, genomes, or brains, and turning this understanding into practical knowledge.”,,, to read more go here: http://www.evolutionnews.org/2012/08/complexity_brak062961.html
And that is the monumental brick wall facing researchers in just trying to understand how an existing organism operates on a day by day, moment by moment, fashion at the molecular level. As to how a single cell on millions of protein molecules transforms itself through embryogenesis into a coherent single living organism containing 100 trillion cells, at a billion trillion protein molecules total, without falling into complete disarray is a miracle upon the miracle of merely existing that is even more astonishing.
HOW BIOLOGISTS LOST SIGHT OF THE MEANING OF LIFE — AND ARE NOW STARING IT IN THE FACE – Stephen L. Talbott – May 2012 Excerpt: “If you think air traffic controllers have a tough job guiding planes into major airports or across a crowded continental airspace, consider the challenge facing a human cell trying to position its proteins”. A given cell, he notes, may make more than 10,000 different proteins, and typically contains more than a billion protein molecules at any one time. “Somehow a cell must get all its proteins to their correct destinations — and equally important, keep these molecules out of the wrong places”. And further: “It’s almost as if every mRNA [an intermediate between a gene and a corresponding protein] coming out of the nucleus knows where it’s going” (Travis 2011),,, Further, the billion protein molecules in a cell are virtually all capable of interacting with each other to one degree or another; they are subject to getting misfolded or “all balled up with one another”; they are critically modified through the attachment or detachment of molecular subunits, often in rapid order and with immediate implications for changing function; they can wind up inside large-capacity “transport vehicles” headed in any number of directions; they can be sidetracked by diverse processes of degradation and recycling… and so on without end. Yet the coherence of the whole is maintained. The question is indeed, then, “How does the organism meaningfully dispose of all its molecules, getting them to the right places and into the right interactions?” The same sort of question can be asked of cells, for example in the growing embryo, where literal streams of cells are flowing to their appointed places, differentiating themselves into different types as they go, and adjusting themselves to all sorts of unpredictable perturbations — even to the degree of responding appropriately when a lab technician excises a clump of them from one location in a young embryo and puts them in another, where they may proceed to adapt themselves in an entirely different and proper way to the new environment. It is hard to quibble with the immediate impression that form (which is more idea-like than thing-like) is primary, and the material particulars subsidiary. Two systems biologists, one from the Max Delbrück Center for Molecular Medicine in Germany and one from Harvard Medical School, frame one part of the problem this way: “The human body is formed by trillions of individual cells. These cells work together with remarkable precision, first forming an adult organism out of a single fertilized egg, and then keeping the organism alive and functional for decades. To achieve this precision, one would assume that each individual cell reacts in a reliable, reproducible way to a given input, faithfully executing the required task. However, a growing number of studies investigating cellular processes on the level of single cells revealed large heterogeneity even among genetically identical cells of the same cell type. (Loewer and Lahav 2011)”,,, And then we hear that all this meaningful activity is, somehow, meaningless or a product of meaninglessness. This, I believe, is the real issue troubling the majority of the American populace when they are asked about their belief in evolution. They see one thing and then are told, more or less directly, that they are really seeing its denial. Yet no one has ever explained to them how you get meaning from meaninglessness — a difficult enough task once you realize that we cannot articulate any knowledge of the world at all except in the language of meaning.,,, http://www.netfuture.org/2012/May1012_184.html#2
And yet Darwinists, apparently completely oblivious to the miracle that is a billion trillion protein molecules all operating in a cohesive fashion to keep their bodies alive, and oblivious to the fact that NO ONE has a clue how that miracle all ‘comes together’ into a cohesive whole, dogmatically pretend as if they know for a fact how all life on Earth originated. In fact wd400 is notorious for proclaiming that 'we just don't understand evolution' like he does.,, Unbounded pride in towering ignorance is a fair assessment of the Darwinian mindset!
Alexander Tsiaras: Conception to birth — visualized – video http://www.youtube.com/watch?v=fKyljukBE70 Mathematician Alexander Tsiaras on Human Development: “It’s a Mystery, It’s Magic, It’s Divinity” – March 2012 Excerpt: ‘The magic of the mechanisms inside each genetic structure saying exactly where that nerve cell should go, the complexity of these, the mathematical models on how these things are indeed done, are beyond human comprehension. Even though I am a mathematician, I look at this with the marvel of how do these instruction sets not make these mistakes as they build what is us. It’s a mystery, it’s magic, it’s divinity.’ -per ENV One Body – animation – video http://www.youtube.com/watch?v=pDMLq6eqEM4 Introduction to Cells – Anatomy – video http://www.youtube.com/watch?v=gFuEo2ccTPA
Verse and Music:
Jeremiah 1:5 "Before I formed you in the womb I knew you,,,, Mandisa - Esther - Born For This - music video http://www.youtube.com/watch?v=ZxFCber4TDo
bornagain77
June 9, 2014
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Thanks for the reply wd400 but as above, please can you point to where in the publication this is stated or explained. If what you are saying is true I would expect 3 things: 1) the percentage to actually be much lower than stated (as per your example above) 2) the larger the slice, the lower the similarity should be (but this does not seem to hold true as per slice size optimisation results?) 3) the results to show disparity to previous published intense results (it seemed to corroborate the MSY alignments published in 2010) If you can show us in that publication where it shows he takes this approach it would be helpful.Dr JDD
June 9, 2014
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The thing you are missing is that tomkins explicitly prevents alignments from including a gap. That combined with the fact only one alignment is kept means he is basically estimating the average gap between indels and rearrangements, not similarly in any normal sensewd400
June 9, 2014
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Thanks Dr JDD: I was going to read through the paper myself to find out exactly what Tomkins did. I have it printed out and next to me. The fact that you've read the paper and analyzed it spares me the labor of doing so. You see, at this point in the Darwinian debates, I have very little interest in doing things like this. Once I had plenty of energy and motivation to do so; but now, with study after study coming out each day that flies in the face of strict Darwinian thought, I don't see the purpose anymore. It's just a matter of time before Darwinism is forced to topple over. ID as a project to "prove" the existence of God, or a Designer, is a non-starter. Science cannot do this; only philosophy and metaphysics can. But, ID as a project pointing to a designing influence on the contents of cells and life in general, this, to some degree, will succeed. Just a matter of time, as I say.PaV
June 9, 2014
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Hi Querius,   Thanks for your comments. I believe the original 98.5% figure came from aligning very small sections of some gene-coding DNA from humans and chimps and extrapolating up the similarity. I may be wrong, but that has always been my impression of the original work to come up with that figure. As you say, quite clearly this is obviously wrong given that simple fact you state, that the differing sizes in the genome exclude the possibility of true overall similarity of 98.5%. You could argue that additional information would be the result that could be expected after divergence from a common ancestor, but again the point is 98.5% is mis-leading and based on the assumption that a lot of apparent non-coding DNA information at the time is now known to have function and not be functionless. Furthermore, I wonder about the implications of the number of true differences between chimp and human DNA and how this fits in with the theory of neutral evolution.   As for wd400’s objections, I have finally had a chance to read through the Tomkins original paper in detail and I do not agree with his assessment of how Tomkins has done this work, nor do I know why he is assuming what Tomkins has done equates to his example. Here are some pertinent quotes from the publication:  
Since the sequence slices below 200 bases produced non-optimal alignments, they were omitted for the rest of the chimp chromosomes (Fig. 1). For chimp chromosomes 5 to 15, and chromosome 18, sequence slice files of 200 to 450 base increments provided a complete range of results to select an optimal query slice. For chimp chromosomes 16, 17, and 19 to 22, sequence slice files of 200 to 650 base increments provided a complete range of results to select an optimal query file string size (10 query files per chromosome). In general, the larger chimp chromosomes, which contained larger stretches of non-coding DNA, had regions of similarity that were on average shorter than the smaller and more gene-dense chimp chromosomes, although there were several exceptions to this trend as discussed below.
  So first you can see Tomkins went to great length to determine the optimal slice size to analyse to ensure the highest percentage alignment (most conservative estimate, where being conservative means they are very similar). He found with some chromosomes, longer stretches and shorter stretches analysed gave lower similarity percentages, so he optimised the slice length for each chromosome’s DNA, whilst not going too small to skew a result.   Further:
The definition of similarity for each chimp chromosome was the amount (percent) of optimally aligned chimp DNA (minus ‘N’s). This definition was considered to be quite conservative because it did not include the amount of human DNA absent in the chimp genome nor does it include chimp DNA that could not be aligned to the human genome assembly—a category of chimp DNA termed “unanchored contigs”. The inclusion of chimp DNA not able to be aligned and anchored to human, although negligible for most chromosomes, would have produced slightly lower overall similarities. Likewise, if the amount of human DNA not present in chimp could have also been factored in, this would have also produced somewhat lower overall chromosome similarities as well.
First thing to note, he uses “optimally aligned” analysis. Therefore, I do not understand how wd400 comes to his conclusion because by definition, the example he gives is clearly not “optimally aligned.” Again, Tomkins was trying to be as conservative as possible here. Further, he stripped N’s from the analysis and this is the correct thing to do as these have no definition of base therefore cannot be said to align. These are removed, so he is not taking that position into account which is the correct and fair way to analyse. Finally, he also did not include stretches of chimp/human DNA that could not be aligned and anchored to its respective comparative genome so again, the percentage given is conservative.  
This data illustrates the fact that gene density is not always a dependable predictor of high similarity between chimp and human DNA. In the past, evolutionists have selectively used certain homologous gene-dense DNA segments between human and chimps to produce high levels of DNA similarity, claiming that it represented genome-wide patterns (Bergman and Tomkins, 2012; Tomkins and Bergman, 2012). This is clearly not always the case, even within gene-dense chromosomes.   Only 69% of the chimpanzee X chromosome was similar to human and only 43% of the Y chromosome.The MSY regions of the chimp and human Y-chromosomes were recently compared in great detail and found to be extremely dissimilar in not only DNA sequence similarity, but also gene content (Hughes et al. 2010). This present study confirms the striking difference between human and chimp Y chromosomes, and indicates that these differences are still being largely understated.   Genome-wide, only 70% of the chimpanzee DNA was similar to human under the most optimal sequence-slice conditions. In fact, this would be considered to be a conservative estimate well within the range of results provided by other recent attempts by Buggs (2008) and Progetto cosmo (2012), mentioned above. One must also keep in mind the fact that the chimpanzee genome assembly is still based largely on the human genomic framework as discussed in detail by author Tomkins in several journal publications (Tomkins, 2011a; Tomkins 2011b). In fact, this current study did not use any of the unanchored chimpanzee sequencing contigs that could not be aligned to the human genome.   Had these additional segments of DNA been included, similarities would have been lowered even further, although only slightly. Furthermore, human DNA not found in chimp was also not included in the comparison—another factor that would have lowered similarity estimates. While, chimpanzees and humans do share many localized protein-coding regions of very high similarity, there is overall an extreme DNA sequence discontinuity between the two genomes, which defies evolutionary time-scales and dogmatic presuppositions about a common ancestor.
  There are some important points in the text quoted above.   Wd400 – could you point me to the methodology or statements in this publication that justify your example as one like what Tomkins used? What is your definition of “optimal alignment” that Tomkins has used that leads you to choose the example you give as an accurate representation of how he performed this analysis? I am genuinely interested how you arrived at this conclusion as I cannot see it myself, although I may be wrong as I may be missing something here. Thanks, JDDr JDD
June 9, 2014
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Dr JDD, According the article, "Comparing the human and chimpanzee genomes: Searching for needles in a haystack" (Ajit Varki1 and Tasha K. Altheide):
The chimpanzee genome sequence is a long-awaited milestone, providing opportunities to explore primate evolution and genetic contributions to human physiology and disease. Humans and chimpanzees shared a common ancestor ?5-7 million years ago (Mya). The difference between the two genomes is actually not ?1%, but ?4%—comprising ?35 million single nucleotide differences and ?90 Mb of insertions and deletions.
However, the chimpanzee genome has about 3.0 Bb (about 18.8k coding genes), while the human genome has about 3.3 Bb (about 21.0k coding genes). Thus, the human genome is about 10-12% larger than the chimpanzee genome. This is admittedly simplistic, but even assuming that the chimpanzee's genome is 100% identical with that of the human genome, which of course it's not, the 10-12% size increase in humans would not result in a 98% agreement. So is the larger size of the human genome simply ignored? -QQuerius
June 8, 2014
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A Listener's Guide to the Meyer-Marshall Debate: Focus on the Origin of Information Question -Casey Luskin - December 4, 2013 Excerpt: "There is always an observable consequence if a dGRN (developmental gene regulatory network) subcircuit is interrupted. Since these consequences are always catastrophically bad, flexibility is minimal, and since the subcircuits are all interconnected, the whole network partakes of the quality that there is only one way for things to work. And indeed the embryos of each species develop in only one way." - Eric Davidson http://www.evolutionnews.org/2013/12/a_listeners_gui079811.htmlbornagain77
June 7, 2014
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Of related interest to the 98.5% similarity myth, is the biased methodology, in 1970's, used in deriving the original 98.5% figure:
Geneticist Jeff Tomkins vs. Evolutionary Biologist who got laughed off stage - August 12, 2013 Excerpt: Tomkins described the origin of the fallacious comparison as a myth that got started in reassociation kinetic methods of comparison in the mid-1970's prior to the advent of modern sequencing techniques (like Illumina and Solexa). Reassociation kinetics was a technique where fragments of chimp and human DNA were mixed in the same chemical soup, and the DNAs that were reasonably similar would pair up, hence we got a biased sampling! https://uncommondescent.com/genetics/icc-2013-geneticist-jeff-tomkins-vs-evolutionary-biologist-who-got-laughed-off-stage/
But what is really interesting about this 'biased sampling' is what Wilson and King themselves said about it
In “Science,” 1975, M-C King and A.C. Wilson were the first to publish a paper estimating the degree of similarity between the human and the chimpanzee genome. This documented the degree of genetic similarity between the two! The study, using a limited data set, found that we were far more similar than was thought possible at the time. Hence, we must be one with apes mustn't we? But…in the second section of their paper King and Wilson honestly describe the deficiencies of such reasoning: “The molecular similarity between chimpanzees and humans is extraordinary because they differ far more than sibling species in anatomy and way of life. Although humans and chimpanzees are rather similar in the structure of the thorax and arms, they differ substantially not only in brain size but also in the anatomy of the pelvis, foot, and jaws, as well as in relative lengths of limbs and digits (38). Humans and chimpanzees also differ significantly in many other anatomical respects, to the extent that nearly every bone in the body of a chimpanzee is readily distinguishable in shape or size from its human counterpart (38). Associated with these anatomical differences there are, of course, major differences in posture (see cover picture), mode of locomotion, methods of procuring food, and means of communication. Because of these major differences in anatomy and way of life, biologists place the two species not just in separate genera but in separate families (39). So it appears that molecular and organismal methods of evaluating the chimpanzee human difference yield quite different conclusions (40).” King and Wilson went on to suggest that the morphological and behavioral between humans and apes,, must be due to variations in their genomic regulatory systems. David Berlinski - The Devil's Delusion - Page 162&163 Evolution at Two Levels in Humans and Chimpanzees Mary-Claire King; A. C. Wilson - 1975 *of note: anatomically, humans share more similarities with pigs than they do chimps - per Phyorg
And indeed it is found that if you want to generate a fundamentally new body plan then you have to make changes to genomic regulatory regions:
Darwin or Design? - Paul Nelson at Saddleback Church - Nov. 2012 - ontogenetic depth (excellent update) - video Text from one of the Saddleback slides: 1. Animal body plans are built in each generation by a stepwise process, from the fertilized egg to the many cells of the adult. The earliest stages in this process determine what follows. 2. Thus, to change -- that is, to evolve -- any body plan, mutations expressed early in development must occur, be viable, and be stably transmitted to offspring. 3. But such early-acting mutations of global effect are those least likely to be tolerated by the embryo. Losses of structures are the only exception to this otherwise universal generalization about animal development and evolution. Many species will tolerate phenotypic losses if their local (environmental) circumstances are favorable. Hence island or cave fauna often lose (for instance) wings or eyes. http://www.saddleback.com/mc/m/7ece8/ Membrane Patterns Carry Ontogenetic Information That Is Specified Independently of DNA - Jonathan Wells - 2014 Excerpt: Embryo development (ontogeny) depends on developmental gene regulatory networks (dGRNs), but dGRNs depend on pre-existing spatial anisotropies that are defined by early embryonic axes, and those axes are established long before the embryo’s dGRNs are put in place.,,, DNA sequences do not specify the final functional forms of most membrane components. Still less does DNA specify the spatial arrangements of those components. Yet their spatial arrangements carry essential ontogenetic information. The fact that membrane patterns carry ontogenetic information that is not specified by DNA poses a problem for any theory of evolution (such as Neo-Darwinism) that attributes the origin of evolutionary novelties to changes in a genetic program—-whether at the level of DNA sequences or dGRNs. http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2014.2
Moreover these regulatory regions are found to be very different:
Evolution by Splicing – Comparing gene transcripts from different species reveals surprising splicing diversity. – Ruth Williams – December 20, 2012 Excerpt: A major question in vertebrate evolutionary biology is “how do physical and behavioral differences arise if we have a very similar set of genes to that of the mouse, chicken, or frog?”,,, A commonly discussed mechanism was variable levels of gene expression, but both Blencowe and Chris Burge,,, found that gene expression is relatively conserved among species. On the other hand, the papers show that most alternative splicing events differ widely between even closely related species. “The alternative splicing patterns are very different even between humans and chimpanzees,” said Blencowe.,,, http://www.the-scientist.com/?articles.view%2FarticleNo%2F33782%2Ftitle%2FEvolution-by-Splicing%2F "Where (chimps and humans) really differ, and they differ by orders of magnitude, is in the genomic architecture outside the protein coding regions. They are vastly, vastly, different.,, The structural, the organization, the regulatory sequences, the hierarchy for how things are organized and used are vastly different between a chimpanzee and a human being in their genomes." Raymond Bohlin (per Richard Sternberg) - 9:29 minute mark of video http://www.metacafe.com/watch/8593991/
Thus, where the differences are greatest is exactly where changes are least like to be tolerated, yet it is exactly in these drastically different regions that Darwinism needs flexibility the most. Thus, like the old joke, Darwinists are like the drunk looking for his keys under the streetlamp because the light is better there even though that is not where he lost them. Of note to Wilson and King's observation of many anatomical differences between humans and chimps,, it is interesting to note that so great are the anatomical differences between humans and chimps that a Darwinist actually proposed that a chimp and pig mated with each other and that is what ultimately gave rise to humans:
A chimp-pig hybrid origin for humans? - July 3, 2013 Excerpt: Dr. Eugene McCarthy,, has amassed an impressive body of evidence suggesting that human origins can be best explained by hybridization between pigs and chimpanzees. Extraordinary theories require extraordinary evidence and McCarthy does not disappoint. Rather than relying on genetic sequence comparisons, he instead offers extensive anatomical comparisons, each of which may be individually assailable, but startling when taken together.,,, The list of anatomical specializations we may have gained from porcine philandering is too long to detail here. Suffice it to say, similarities in the face, skin and organ microstructure alone is hard to explain away. A short list of differential features, for example, would include, multipyramidal kidney structure, presence of dermal melanocytes, melanoma, absence of a primate baculum (penis bone), surface lipid and carbohydrate composition of cell membranes, vocal cord structure, laryngeal sacs, diverticuli of the fetal stomach, intestinal "valves of Kerkring," heart chamber symmetry, skin and cranial vasculature and method of cooling, and tooth structure. Other features occasionally seen in humans, like bicornuate uteruses and supernumerary nipples, would also be difficult to incorporate into a purely primate tree. http://phys.org/news/2013-07-chimp-pig-hybrid-humans.html
Moreover, Physorg published a subsequent article showing that the pig-chimp hybrid theory for human origins is much harder to shoot down than Darwinists had first supposed it would be:
Human hybrids: a closer look at the theory and evidence - July 25, 2013 Excerpt: There was considerable fallout, both positive and negative, from our first story covering the radical pig-chimp hybrid theory put forth by Dr. Eugene McCarthy,,,By and large, those coming out against the theory had surprisingly little science to offer in their sometimes personal attacks against McCarthy. ,,,Under the alternative hypothesis (humans are not pig-chimp hybrids), the assumption is that humans and chimpanzees are equally distant from pigs. You would therefore expect chimp traits not seen in humans to be present in pigs at about the same rate as are human traits not found in chimps. However, when he searched the literature for traits that distinguish humans and chimps, and compiled a lengthy list of such traits, he found that it was always humans who were similar to pigs with respect to these traits. This finding is inconsistent with the possibility that humans are not pig-chimp hybrids, that is, it rejects that hypothesis.,,, http://phys.org/news/2013-07-human-hybrids-closer-theory-evidence.html
The obvious question for me is, of course, since Darwinists are having such a hard time proving that we did not come from pig-chimp hybrids, what makes Darwinists so sure that we evolved from apes or anything else in the first place? Any reasonable person would realize that if such a dubious theory as the pig-chimp hybrid theory can cause such havoc, for what was suppose to be such well established science, then perhaps the Darwinian theory for human origins is not nearly as strong as Darwinists have dogmatically held it to be in the first place. Some might even hold that such 'flimsiness' would clearly indicate the original theory was rubbish as to being hard science. Verse and Music:
Jeremiah 1:5 "Before I formed you in the womb I knew you,,,, Mandisa - Esther - Born For This - music video http://www.youtube.com/watch?v=ZxFCber4TDo
bornagain77
June 7, 2014
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Sure - there is no One True Similarity measure. If you want to include all the bases missing in one species in present in other as dissimilarity that's perfectly reasonable, and that's how you end up with ~95%. But then you'd have to realise that far fewer mutatoins are required to explain the indel differences than the single nucleotide differences, so 95% is not such a great gap. I do understand what a reading frame is. I'll repeat myself one last time -- almost none of the genome is protein coding and if Tomkins had wanted to say that small nucleotide differences can make large partical differences that's what he should have said instead of claiming large nucleotide differences. You mention the Y-chromosome, without poingting out this stufdy is on the non-recombining portion of the Y which is subject to very different evolutionary pressures that the rest of the genome as it can't recombine (so the effects of selection are global) and it's full of male-specific geneswd400
June 7, 2014
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wd400 I agree that the example you give is not 60% but I do not know how closely this relates to how Tomkins did it and seems to me a simplistic way of looking at it. The converse problem is when you get things like this: ATCGGCTCGCCATAATCAT ATCGG------ATATTCAT Where historically those would give only 1 mis alignment base as the analysis refuses to take into account indels when making comparisons. So instead of 1/12 non-identity to me this would be 7/18 non-identity. It seemed to me that Thomkins was taking these, and non-alignable genes into context, as opposed to the example you give above. But I may be wrong there, Tomkins would be best to answer that. However, the point still remains about indels as often they are not simply 1 base indel. Additionally, to ignore genes present in one organism but not another and not include those in the comparison you must accept is a biased view, especially as those genes are likely to contribute to how/why we are different, which is the whole point of genomic comparisons. You would expect 2 different models of a car to have many similar components, but the extra/different ones are what make them the unique car. To ignore indels (which have been shown to have function often) and novel genes/orphans etc, seems silly in a true "comparison". Furthermore, in the example you show above if in an exonic region that 1 insertion would cause a complete frameshift changing that protein. Often this is OK if near the end of the sequence/domain however would likely be detrimental to its function if elsewhere, meaning even if it had function it would likely be very different to the one you are comparing it to, if it actually was a working gene. Finally, it is well established among non-creationists that the Chimp and human Y-chromosome are quite remarkably different. I do not know how much indepth similar analysis has been done for other chromosomes though: http://www.ncbi.nlm.nih.gov/pubmed/20072128
Surprisingly, however, > 30% of chimpanzee MSY sequence has no homologous, alignable counterpart in the human MSY, and vice versa.... ...Indeed, at six million years of separation, the difference in MSY gene content in chimpanzee and human is more comparable to the difference in autosomal gene content in chicken and human, at 310 million years of separation Also, much of the chimp genome and other primates are put together on a human template essentially which is heavily biased.
Dr JDD
June 7, 2014
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Red Herrings??? Stuffing Herrings in your empty head??? Why would you suggest such things??? :) Excuse me, but you guys are the ones arguing for 98.5% similarity and yet, contrary to the fictitious sequence wd400 pulled out of his, errr, imagination, ,,,
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 From Jerry Coyne, More Table-Pounding, Hand-Waving - May 2012 Excerpt: "More than 6 percent of genes found in humans simply aren't found in any form in chimpanzees. There are over fourteen hundred novel genes expressed in humans but not in chimps." Jerry Coyne - ardent and 'angry' neo-Darwinist - professor at the University of Chicago in the department of ecology and evolution for twenty years. He specializes in evolutionary genetics. http://www.evolutionnews.org/2012/05/from_jerry_coyn060271.html "However, with the advent of sequencing of full genomes, it became clear that approximately 20–40% of the identified genes could not be associated with a gene family that was known before. Such genes were originally called ‘orphan’ genes" http://ccsb.dfci.harvard.edu/web/export/sites/default/ccsb/publications/papers/2013/Tautz_eLS_2013.pdf 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 Study Reports a Whopping "23% of Our Genome" Contradicts Standard Human-Ape Evolutionary Phylogeny - Casey Luskin - June 2011 Excerpt: For about 23% of our genome, we share no immediate genetic ancestry with our closest living relative, the chimpanzee. This encompasses genes and exons to the same extent as intergenic regions. We conclude that about 1/3 of our genes started to evolve as human-specific lineages before the differentiation of human, chimps, and gorillas took place. (of note; 1/3 of our genes is equal to about 7000 genes that we do not share with chimpanzees) http://www.evolutionnews.org/2011/06/study_reports_a_whopping_23_of047041.html
Moreover,
Ten years on, still much to be learned from human genome map - April 12, 2013 Excerpt:,,,"What's more, about 10 percent of the human genome still hasn't been sequenced and can't be sequenced by existing technology, Green added. "There are parts of the genome we didn't know existed back when the genome was completed," he said.,,, http://medicalxpress.com/news/2013-04-ten-years-human-genome.html
All in all, Dr. Tomkins sober criticisms against the 'defend until death' 98.5% myth of Darwinists are very well warranted:
Groundbreaking Genetic Discoveries Challenge Ape to Human Evolutionary Theory – June 17, 2013 Excerpt: Dr. Tomkins further emphasized that evolutionists greatly exaggerate the genetic similarities between humans and chimps, and often ignore areas of DNA where major differences do exist. “It’s called cherry-picking the data,” he explained. “There are many genetic regions between humans and chimps that are radically different. In fact, humans have many sections of DNA that are missing in chimps and vice versa. Recent research is now showing that the genomes are only 70% similar overall.”,,, http://christiannews.net/2013/06/17/groundbreaking-genetic-discoveries-challenge-ape-to-human-evolutionary-theory/
Call it a Red Herring and stuff it in your empty head if you want, but I simply see no reason why I, nor anybody else, should put any confidence in what you guys are saying. PS, perhaps one of these days you guys will actually get to dealing with the quantum falsification of the materialistic underpinnings of Darwinian thought?bornagain77
June 7, 2014
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Bornagain 77, you know where you can stuff your red herrings.Piotr
June 7, 2014
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P.S. Many different similarity metrics are possible, and they may yield different percentages (nothing wrong about that as long as the author is clear about what exactly is being measured). If you use the same metric for, say, human vs. chimp, human vs. macaque, and chimp vs. macaque genomes, it's a safe bet that Homo and the chimpanzee will consistently turn out to be more similar to each other than either is to macaques. What really counts, however, is not how close a given similarity metric is to 100%, but whether similarities and differences are structured hierarchically (reflecting phylogenetic relationships). And yes, they are.Piotr
June 7, 2014
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Piotr asks:
Can’t you see through these tricks?
Which I find to be a VERY ironic thing for a Darwinist to say. The whole theory is based on smoke and mirrors, where, as Dr. Hunter has pointed out numerous times, all contradictory evidence is magically turned into evidence supporting Darwinism. Well contrary to what Piotr and wd400 would prefer to believe, There are many people, including one of the co-developers of the method used to analyze genetic similarities between species, and even he said, in 2002, that the 98.5% figure should be revised downward to 95 percent. The situation has only gotten worse since 2002. Even Jerry Coyne, certainly no friend to ID, admitted that over 1400 hundred genes (6%) have no counterpart in chimps and are 'ORFans'. Thus, subtracting 6% from 95%, the 89% figure is reached using numbers that Darwinists themselves have supplied! Moreover, there are good reasons for doubting Darwinian presuppositions of non-functionality are true.,,, For instance, synonymous mutations which spelled for the same amino acid within the genetic code were thought by Darwinists to be of no effect, but, as would be presupposed from a design perspective, it was found that even synonymous mutations can have a pronounced effect:
Synonymous Codons: Another Gene Expression Regulation Mechanism - September 2010 Excerpt: There are 64 possible triplet codons in the DNA code, but only 20 amino acids they produce. As one can see, some amino acids can be coded by up to six “synonyms” of triplet codons: e.g., the codes AGA, AGG, CGA, CGC, CGG, and CGU will all yield arginine when translated by the ribosome. If the same amino acid results, what difference could the synonymous codons make? The researchers found that alternate spellings might affect the timing of translation in the ribosome tunnel, and slight delays could influence how the polypeptide begins its folding. This, in turn, might affect what chemical tags get put onto the polypeptide in the post-translational process. In the case of actin, the protein that forms transport highways for muscle and other things, the researchers found that synonymous codons produced very different functional roles for the “isoform” proteins that resulted in non-muscle cells,,, In their conclusion, they repeated, “Whatever the exact mechanism, the discovery of Zhang et al. that synonymous codon changes can so profoundly change the role of a protein adds a new level of complexity to how we interpret the genetic code.”,,, http://www.creationsafaris.com/crev201009.htm#20100919a
Thus, even for a supposed minor variation, Darwinian presuppositions about functionality were, to put it mildly, misleading as to what was actually found. This is not an anomaly at the edges either that I'm picking on. Darwinian presuppositions about non-functionality have been a major hindrance throughout its history. From vestigial organs to the current fiasco with 'Junk' DNA, Darwinian presuppositions about non-functionality have been a hindrance to research. After decades and decades of such tripe from the pseudo-science that is Darwinian evolution, we can turn Piotr's question around to himself and ask of him 'Can’t you see through these tricks?'bornagain77
June 7, 2014
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Of course "Tomkins asserts that he did indeed take into account gaps". The method he described in his papers works exactly as I have illustrated. I guess it's left as an exercise to the reader to decide what Tomkins means by "accounts for". The most charitable interpretation is that he means gaps are counted as differences -- which is definitely true!wd400
June 7, 2014
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Querius: This is what Tomkins says in his article, in the section "Genome Comparison Philosophy and Approach" (emphasis added):
Given that the genome-wide analyses required a large amount of cumulative and comparative data, only the top alignment for each database hit (if it existed) was returned. Gapping was disallowed for a variety of reasons. First, Altschul et al. (1990) determined that the addition of gapping strategies for alignments designed to locate regions of local similarity using BLAST was negligible. Secondly, an objective comparison among all queries negates the use of gapping with the algorithm. Finally, the top local pair-wise alignments that were obtained involved a variety of very liberal to very stringent matching parameters for word size and e-value.
This means that (1) if there were two or more alignments per database hit, only one was taken into account; (2) indels weren't included (only non-gapped alignments counted). In his statement, Tomkins "says a thing which is not", as the Hounyhnhnms would put it. Can't you see through these tricks? What's wrong your reading comprehension skill, folks?Piotr
June 7, 2014
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bornagain77@159 posted
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.
After which Piotr@162 chortled to 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.
Apparently, Piotr's mind is made up, regardless of any information to the contrary. In his last sentence, I believe that "ale" should be "are." What is it about Tomkin's statement, "My data not only takes into account gaps, but sequences present in human and absent in chimp, and vice versa," that Piotr and wd400 cannot bring themselves to accept? Note, I'm not saying that they should accept Tomkin's conclusions, but simply to admit that Tomkins asserts that he did indeed take into account gaps. -QQuerius
June 7, 2014
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