The Evolutionary Tree is Imaginary
“The problem with those who are unable to see evolution, is that they don’t have imaginations.” (Gail E. Kennedy, Ph.D., Associate Professor, Anthropology, UCLA)
Darwn's "Tree of Life" is soley imaginary and scientists can't construct it because the evidence contradicts a single evolutionary tree.
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- ‘The tree diagram itself is ingrained in our research culture, our training, and our textbooks. It currently dominates the recognition and interpretation of patterns in genetic data. However, many patterns in these data cannot be represented accurately by a tree ...the more we learn about genomes the less tree-like we find their evolutionary history to be. ...Tree-based genomic analysis is proving to be an accuracy challenge for the evolutionary biology community, and although genome-scale data carry the promise of fascinating insights into treelike processes, non-treelike processes are commonly observed." (Bapteste et al., Networks: expanding evolutionary thinking, Trends in Genetics, August 2013, http://bioinfo.cs.rice.edu/sites/bioinfo.cs.rice.edu/files/TIG2013.pdf
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- "Many biologists now argue that the tree concept is obsolete and needs to be discarded. “We have no evidence at all that the tree of life is a reality,”...Syvanen recently compared 2000 genes that are common to humans, frogs, sea squirts, sea urchins, fruit flies and nematodes. In theory, he should have been able to use the gene sequences to construct an evolutionary tree showing the relationships between the six animals. He failed. The problem was that different genes told contradictory evolutionary stories." (Graham Lawton,Why Darwin was wrong about the tree of life," New Scientist, January 21, 2009, http://www.newscientist.com/article/mg20126921.600-why-darwin-was-wrong-about-the-tree-of-life.html
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- "[S]cientists started analyzing a variety of genes from different organisms and found that their relationship to each other contradicted the evolutionary tree of life derived from rRNA analysis alone." (James A Lake, Ravi Jain, Maria C Rivera, "Mix and Match in the Tree of Life", Science, Vol. 283 no. 5410 pp. 2027-2028, 26 March 1999, http://www.sciencemag.org/content/283/5410/2027
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- "I’ve looked at thousands of microRNA genes, and I can’t find a single example that would support the traditional tree,” ...The technique “just changes everything about our understanding of mammal evolution”...a chance investigation of microRNAs in microscopic creatures called rotifers led him to examine these regulatory molecules in everything from insects to sea urchins. And as he continues to look, he keeps uncovering problems, from the base of the animal tree all the way up to its crown. ...When Peterson started his work on the placental phylogeny, he had originally intended to validate the traditional mammal tree, not chop it down. As he was experimenting with his growing microRNA library, he applied it to mammals because their tree was so well established that they seemed an ideal test. Alas, the data didn’t cooperate. ...“The microRNAs are totally unambiguous,” he says, “but they give a totally different tree from what everyone else wants.” ... 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,” (Rewriting Evolution, Nature, Vol 486, 28 June 2012, http://www.nature.com/polopoly_fs/1.10885%21/menu/main/topColumns/topLeftColumn/pdf/486460a.pdf
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- "In the quest to reconstruct the Tree of Life, researchers have increasingly turned to phylogenomics, the inference of phylogenetic relationships using genome-scale data (Box 1). Mesmerized by the sustained increase in sequencing throughput, many phylogeneticists entertained the hope that the incongruence frequently observed in studies using single or a few genes [1] would come to an end with the generation of large multigene datasets. Yet, as so often happens, reality has turned out to be far more complex, as three recent large-scale analyses, one published in PLoS Biology [2]–[4], make clear. The studies, which deal with the early diversification of animals, produced highly incongruent (Box 2) findings despite the use of considerable sequence data (see Figure 1). Clearly, merely adding more sequences is not enough to resolve the inconsistencies." (Hervé Philippe1*, Henner Brinkmann1, Dennis V. Lavrov2, D. Timothy J. Littlewood3, Michael Manuel4, Gert Wörheide5,6, Denis Baurain7, Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough, March 2011 Issue of PLOS Biology, http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000602
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- “Molecular phylogenists will have failed to find the ‘true tree,’ not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree.” (W. Ford Doolittle, "Phylogenetic Classification and the Universal Tree," Science, Vol. 284:2124-2128, June 25, 1999, http://www.sciencemag.org/content/284/5423/2124.abstract
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- "With more and more sequences available, it turned out that most protein phylogenies contradict each other as well as the rRNA trees" (H. Philippe and P. Forterre, The Rooting of the Universal Tree of Life Is Not Reliable, Journal of Molecular Evolution, 49:509–523, 1999, http://www.ncbi.nlm.nih.gov/pubmed/10486008
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- “Phylogenetic incongruities can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves.” (Carl Woese "The Universal Ancestor," Proceedings of the National Academy of Sciences USA, Vol. 95:6854-9859, June, 1998, http://www.pnas.org/content/95/12/6854.full
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- "A major challenge for incorporating such large amounts of data into inference of species trees is that conflicting genealogical histories often exist in different genes throughout the genome." (James H. Degnan and Noah A. Rosenberg, Gene tree discordance, phylogenetic inference and the multispecies coalescent, http://www.stanford.edu/group/rosenberglab/papers/DegnanRosenberg2009-TREE.pdf
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- A List of Genomes that Just Don't Fit: (Nov 29, 2013, http://kgov.com/list-of-genomes-that-just-dont-fit
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- "The genes FOXP2, FOXP1, FOXP3 and FOXP4 render different phylogenetic trees. Dawkins specifically mentioned the FOXP2 gene and this gene tree shows Gorilla most closely related to Mouse Lemur and no where near Human or Chimp so that alone refutes his claim to a perfect branching tree." (Dawkins Best Evidence Refuted, Jan 13, 2012, http://www.youtube.com/watch?v=IfFZ8lCn5uU
) "[T]the FOXP2 gene in Humans is considerably more similar to that in Dolphins, Rabbits, Sloths, Horses, Pandas, Vampire Bats, Dogs, Opossums, Pigs, Finches, Squirrels, Rats, Chickens, Elephants, Zebrafish, Cows, Platypus, Anole Lizard, Guinea Pigs, Armadillos and Turkeys (in that order from most to least similar) THAN IT IS IN GORILLA!!! So, there is NO "perfect branching tree", as we watch the nested hierarchy go down the toilet. Why is FOXP2 gene in Humans more similar to that in Platypus, Chickens and Fish than Gorillas??? That's simple. BECAUSE we have NO COMMON ANCESTOR." (Dawkins Caught Lying for Darwin, http://www.youtube.com/watch?v=vnYik52Y5rI
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- "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." (Liliana M. Dávalos, Andrea L. Cirranello, Jonathan H. Geisler, and Nancy B. Simmons, Understanding phylogenetic incongruence: lessons from phyllostomid bats, Biological Reviews of the Cambridge Philosophical Society, Vol. 87, 2012, http://www.ncbi.nlm.nih.gov/pubmed/22891620
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- "Historical patterns of species diversity inferred from phylogenies typically contradict the direct evidence found in the fossil record... This striking inconsistency between phylogenies and fossils limits our understanding of macroevolution, and it undermines our confidence in phylogenetic inference" (Morlon H, Parsons TL, Plotkin JB., Reconciling molecular phylogenies with the fossil record, 2011 Sep 27, http://www.ncbi.nlm.nih.gov/pubmed/21930899
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- “Despite increasing methodological sophistication, phylogenies derived from morphology, and those inferred from molecules, are not always converging on a consensus.” (Matthew A. Wills, "The tree of life and the rock of ages: are we getting better at estimating phylogeny," BioEssays, Vol. 24: 203-207 (2002), reporting on the findings of Michael J. Benton, "Finding the tree of life: matching phylogenetic trees to the fossil record through the 20th century," Proceedings of the Royal Society of London B, Vol. 268: 2123-2130, 2001, http://onlinelibrary.wiley.com/doi/10.1002/bies.10065/abstract
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- And, phylogenetic conflict is common, and seems to be the norm rather than the exception. “Evolutionary trees constructed by studying biological molecules often don’t resemble those drawn up from morphology.” (Trisha Gura, “Bones, Molecules or Both?,” Nature, Vol. 406:230-233, July 20, 2000, http://www.nature.com/nature/journal/v406/n6793/full/406230a0.html
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- "In conclusion, the biological processes that generate phylogenetic conflict are ubiquitous [constantly encountered, widespread], and overcoming incongruence requires better models and more data than have been collected even in well-studied organisms such as phyllostomid bats." (Understanding phylogenetic incongruence: lessons from phyllostomid bats, Nov. 2012, http://www.ncbi.nlm.nih.gov/pubmed/22891620
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Because the evidence contradicts, evolutionary scientists use ad hoc rationalizations to make the evidence "fit" into the Neo-Darwinian story.
- "The truth is that common ancestry is merely an assumption that governs interpretation of the data, not an undeniable conclusion, and whenever data contradicts expectations of common descent, evolutionists resort to a variety of different ad hoc rationalizations to save common descent from being falsified. Some of these ad hoc rationalizations may appear reasonable — horizontal gene transfer, convergent evolution, differing rates of evolution (rapid evolution is conveniently said to muddy any phylogenetic signal) [Who could know, the rates of evolution without already having in mind a picture of how the evolutionary story was supposed to unfold], fusion of genomes — but at the end of the day, we must call them what they are: ad hoc rationalizations designed to save a theory that has already been falsified. Because it is taken as an assumption, evolutionists effectively treat common ancestry in an unfalsifiable and unscientific fashion, where any data that contradicts the expectations of common descent is simply explained away via one of the above ad hoc rationalizations. But if we treat common descent as it ought to be treated — as a testable hypothesis — then it contradicts much data." (Casey Luskin, A Primer on the Tree of Life, May 12, 2009, http://www.discovery.org/a/10651
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"Maybe the reason that different genes yield different evolutionary trees is because there isn't a single unified tree of life to be found. In other words, perhaps universal common ancestry is simply wrong." (Casey Luskin, Nature Article Finds MicroRNAs are "Tearing Apart Traditional Ideas about the Animal Family Tree", June 29, 2012, http://www.evolutionnews.org/2012/06/nature_article061471.html
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Futhermore, a third of genes, called orphan genes, have been found in every genome sequenced, seem to have no parents or family of any kind. Where do they come from? With no obvious ancestry, it was as if these genes appeared out of nowhere!
- "When biologists began sequencing genomes they discovered up to a third of genes in each species seemed to have no parents or family of any kind. ...But as the genomes of more and more organisms were sequenced, genetic family reunions proved to be the exception rather than the rule. Orphan genes have since been found in every genome sequenced to date, from mosquito to man, roundworm to rat, and their numbers are still growing." (Helen Pilcher, Genes from nowhere: Orphans with a surprising story, 16 January 2013, http://ccsb.dfci.harvard.edu/web/export/sites/default/ccsb/publications/papers/2013/All_alone_-_Helen_Pilcher_New_Scientist_Jan_2013.pdf
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- "[E]very evolutionary lineage harbours orphan genes that lack homologues in other lineages and whose evolutionary origin is only poorly understood." (Tautz D, Domazet-Lošo T., The evolutionary origin of orphan genes, 2011 Aug 3, http://bioinfo2.ugr.es/PDFsClase/EvolMol/The%20evolutionary%20origin%20of%20orphan%20genes_2011.pdf
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- "Perhaps we see so many species- and clade-specific orphan genes because they are uniquely designed for species- and clade-specific functions. Certainly, this runs contrary to the expectation of common descent." (Ann Gauger, Orphan Genes: A Guide for the Perplexed, July 30, 2013, http://www.evolutionnews.org/2013/07/orphan_genes_a074971.html#sthash.p6Xzk8DX.dpuf
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The evidence highly likely supports many trees/bushes/webs [polyphyletic], rather than one evolutionary tree [monophyletic].
- Many traits of living creatures are allocated so unsystematically that, with increasing research, it becomes, not simpler, but more difficult to draw up consistent family trees and to reconstruct non-contradictory genealogical relationships. Instead of family trees, continuously new, stand-alone family bushes must be drafted. There is also the fact that modern DNA analyses force us to revise already accepted genealogical trees and to represent them once again as individual bushes. The creation of a generally acknowledged family tree of species has failed. By drafting a single family tree of life (monophyletic representation), one is attempting to trace the origins of different forms of life (basic types) back to a single common ancestor. If, on the other hand, one talks of family bushes (polyphyletic representation), one means a plurality of individual lineages, which cannot be traced back to a single common ancestor. (Reinhard Junker und Siegfried Scherer, Evolution, ein kritisches Lehrbuch, 2006, page 247.). In the past, one relied on drawing up family trees on the basis of anatomical and physiological features and characteristics of reproduction and behavior. Even then, it was often difficult to categorize the diversely distinctive genera, families and species of plants and animals in an unambiguous classification. Today, modern research also has the analysis of genetic makeup (DNA) at its disposal. Up until a few years ago, it was hoped that these DNA analyses would provide confirmation of the then-current family genealogical tree structures. These hopes were, however, quite unequivocally not fulfilled. The opposite was the case. Instead of the hoped for family tree, the designation of new family bushes came, ever increasingly, to the forefront. Family tree research in fossils: In spite of intensive research, to date not a single sequence of fossils has been found, which starts with the invertebrate and progresses via fishes, amphibians and reptiles to mammals. (Vij Sodera, One Small Speck to Man, the Evolution Myth, Vija Sodera Productions, 2003, page 37.)
- "We already have good evidence that linear descent with modification is false for prokaryotes, because their tree looks like a thicket. At what point will molecular systematists be willing to say that at the root of the animal phyla we have not one tree but a grove?" (Ann Gauger, Confusing Similarity with Evolutionary History, Biologic Institute, December 16 2012, http://www.biologicinstitute.org/post/38126556097/confusing-similarity-with-evolutionary-history
- Even Dr. Craig Venter, an American Biologist, denied common descent! "I think the tree of life is an artifact of some early scientific studies that aren't really holding up." (Dr. Craig Venter Denies Common Descent in front of Richard Dawkins! May 24, 2013, http://www.youtube.com/watch?v=MXrYhINutuI
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- Back in 1999, Malcolm S. Gordon, a Professor of Biology, stated: “Do traceable lines of descent exist that might ultimately permit characterization of the genomes of organisms basal to the clades for the highest categories? The answer to this question increasingly appears to be no. Recent work on genomic structures demonstrate that all living organisms are genetic composites: mosaics and chimeras composed of bits and pieces of multiple genomes derived from multiple sources. …The base of the universal tree of life appears not to have been a single root, but was instead a network of inextricably intertwined branches deriving from many, perhaps 100 or more, genetic sources.” (Malcolm S. Gordon, “The Concept of Monophyly: A Speculative Essay Biology and Philosophy 14 (1999):331-348, http://www.arn.org/docs/odesign/od201/ls201.htm
) http://www.the-aps.org/mm/Membership/Living-History/gordon/GordonCV.pdf
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