Evolution is Getting Slammed Again in This Transcription Factor Research

_{Cornelius Hunter

January 28, 2013

Intelligent Design}

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New research on how certain transcription factors work together is causing major problems for the theory of evolution. Transcription factors are proteins that attach to DNA and turn genes on or off. These regulatory proteins have recently been promoted to star status by evolutionists because their expectation that evolution proceeds by creating new proteins has fallen short. Instead of creating new proteins, our modern-day Epicureanism is now supposed to have reprogrammed how existing proteins are used in a mind boggling circuitry of molecular regulators, of which transcription factors play a major role. As one evolutionist explained: Read more

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Intelligent Design Prediction: One day humans will engineer a chromosomal fusion.Mung_{January 30, 2013
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Why The Chromosomal Fusion Argument Doesn’t Wash - Jonathan M - February 2011 https://uncommondescent.com/intelligent-design/why-the-chromosomal-fusion-argument-doesnt-wash/ It's Cherry Picking Season - July 24, 2012 Excerpt (Guy walks into a bar and thinks he is a chimp): I try to outline all the functions of telomeric repeats, but my friend tells me that I am getting off the subject. He wants to me to focus on the ITSs, the tracks of the hexamer TTAGGG that reside within chromosome arms or around the centromere, not at the ends. I tell him that I was just coming to that topic. The story, you see, is that in the lineage leading up (or down, I forget which) to chimps and humans, a fusion of chromosome ends occurred -- two telomeres became stuck together, the DNA was stitched together, and now we find the remnants of this event on the inside of chromosomes. And to be fair, I concede at this point that the 2q13 ITS site shared by chimps and humans can be considered a synapomorphy, a five-dollar cladistic term meaning a genetic marker that the two species share. As this is said, it is apparent that the countenance of my acquaintance lightens a bit only to darken a second later. For I follow up by saying that of all the known ITSs, and there are many in the genomes of chimps and humans, as well as mice and rats and cows..., the 2q13 ITS is the only one that can be associated with an evolutionary breakpoint or fusion. The other ITSs, I hasten to add, do not square up with chromosomal breakpoints in primates (Farré M, Ponsà M, Bosch M. 2009, "Interstitial telomeric sequences (ITSs) are not located at the exact evolutionary breakpoints in primates," Cytogenetic and Genome Research 124(2): 128-131.). In brief, to hone in on the 2q13 ITS as being typical of what we see in the human and chimp genomes seems almost like cherry-picking data. Most are not DNA scars in the way they have been portrayed. http://www.evolutionnews.org/2012/07/its_cherry_pick_1062491.html The chromosome 2 fusion model of human evolution—part 1: re-evaluating the evidence - Jerry Bergman and Jeffrey Tomkins Conclusion: The purportedly overwhelming DNA evidence for a fusion event involving two primate chromosomes to form human chromosome 2 does not exist, even without the aid of new analyses. In this report, our review of only the reported data by evolutionary scientists shows that the sequence features encompassing the purported chromosome-2 fusion site are far too ambiguous to infer a fusion event. In addition to a lack of DNA sequence data for a head-to-head chromosomal fusion, there also exists a decided paucity of data to indicate a cryptic centromere. In a companion paper (part 2) to this, we report the results of additional data analyses using a variety of bioinformatic tools and publicly available DNA sequence resources that further refute the hypothetical chromosome fusion model. http://creation.com/chromosome-2-fusion-1 What I Said about Chromosomal Fusion and Why I Said It - David Klinghoffer - July 23, 2012 Excerpt: [T]he evidence for chromosomal fusion isn't nearly as clear-cut as evolutionists like [Kenneth] Miller claim. Telomeric DNA at the ends of our chromosomes normally consists of thousands of repeats of the 6-base-pair sequence TTAGGG. But the alleged fusion point in human chromosome 2 contains far less telomeric DNA than it should if two chromosome were fused end-to-end: As evolutionary biologist Daniel Fairbanks admits, the location only has 158 repeats, and only "44 are perfect copies" of the sequence.46 Additionally, a paper in Genome Research found that the alleged telomeric sequences we do have are "degenerated significantly" and "highly diverged from the prototypic telomeric repeats." The paper is surprised at this finding, because the fusion event supposedly happened recently -- much too recent for such dramatic divergence of sequence. Thus the paper asks: "If the fusion occurred within the telomeric repeat arrays less than ?6 mya [million years ago], why are the arrays at the fusion site so degenerate?"47 The conclusion is this: If two chromosomes were fused end-to-end in humans, then a huge amount of alleged telomeric DNA is missing or garbled. Finally, the presence of telomeric DNA within a mammalian chromosome isn't highly unusual, and does not necessarily indicate some ancient point of fusion of two chromosomes. Evolutionary biologist Richard Sternberg points out that interstitial telomeric sequences (ITSs) are commonly found throughout mammalian genomes, but the telomeric sequences within human chromosome 2 are cherry-picked by evolutionists and cited as evidence for a fusion event.... http://www.evolutionnews.org/2012/07/what_i_said_abo_1062451.html What the Literature Says about Chromosomal Fusion and Why It Says It - Casey Luskin July 24, 2012 http://www.evolutionnews.org/2012/07/what_the_litera_1062521.html Here is a good summary of why the chromosome 2 argument does not wash https://uncommondescent.com/intelligent-design/spring-it-on-em-and-watch-the-fur-fly/#comment-431951bornagain77_{January 30, 2013
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lol Obviously the fusion required a designer.Mung_{January 29, 2013
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Speaking of chimpanzees, how are ID-ers dealing with the fusion of two chimp chromosomes to make our number 2 chromosome as mentioned by Ken Miller?Davem_{January 29, 2013
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Dr. Hunter. what is the difference, or relationship, between these transcriptions factors and methyl tagging? thanksMung_{January 28, 2013
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Pardon my sloppy com - - - I was replying to BA77's remark (#4) concerning the upcoming debate between Craig and Rosenberg.owendw_{January 28, 2013
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Brings to mind this: http://edwardfeser.blogspot.com/2012/05/rosenberg-roundup.html Feser - from his lengthy, multi-part review of Rosenberg's "The Atheist's Guide to Reality." --- "The difference between us is this: Rosenberg acknowledges that the implications in question are utterly bizarre, but maintains that they must be accepted because the case for the scientism that entails them is ironclad. I maintain that Rosenberg’s case for scientism is completely worthless, and that the implications of scientism are not merely bizarre but utterly incoherent and constitute a reductio ad absurdum of the premises that lead to them." Could be an interesting debate, but I'd rather hear Feser vs Rosenberg . . .owendw_{January 28, 2013
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OT: Atheistic Science is Rapidly Sinking in the Quicksand - January 28, 2013 - Rabbi Moshe Averick http://www.algemeiner.com/2013/01/28/atheistic-science-is-rapidly-sinking-in-the-quicksand/bornagain77_{January 28, 2013
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OT: Upcoming William Lane Craig debate this friday Feb 1 Is Faith in God Reasonable? Debate: Alex Rosenburg vs. William Lane Craig - video You may sign up to watch the live debate for free here http://live.biola.edu/ Overview of debate: What hath Jerusalem to do with Athens? Or what hath faith to do with reason? Drs. William Lane Craig and Alex Rosenberg will debate this all important and pervasive question concerning the reasonableness of faith in God. The nature of the question in this debate is no mere academic matter. The question of God is the most important question. One’s answer to it will impact nearly all other beliefs one holds from common notions of morality to politics and from our interest and investigation of our world to what we take to be our purpose(s) in life. Is “faith” foolish? By this, should it be understood to be blind? Or is it reasonable and, if so, by what measure and to whom is it foolishness? For many, Mark Twain is right on the mark when he said that “Faith is believing something you know ain’t true.” Yet the great thinkers of Judaism and Christianity like Philo, Moses Maimonides, Thomas Aquinas, and John Calvin considered faith to be an extraordinarily important virtue (moral and/or intellectual)! Indeed, it is not only the condition by which salvation is appropriated in these Abrahamic faith traditions (which are taken by insiders to actually be knowledge traditions), but it is the basis for movements from Mother Teresa’s compassion and our concern for the poor to Isaac Newton’s inspiration in science in light of God’s creation of the world and man being made in God’s image. Is faith in God reasonable? Ought we to have faith in God?bornagain77_{January 28, 2013
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OT: The Edge of Evolution (Michael Behe) - radio interview http://www.youtube.com/watch?v=eP0LN63b8qY Sites which responded to the criticisms of "The Edge' are listed in the video description:bornagain77_{January 28, 2013
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In supplemental note, it is turning out, besides finding that "that most alternative splicing events differ widely between even closely related species", it is also found that the specific gene sets per species, though while roughly similar in total gene number (in the low tens of thousands per species), are turning out to be far more 'species specific' than we were originally led to believe: Genes from nowhere: Orphans with a surprising story - 16 January 2013 - Helen Pilcher Excerpt: 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. Nevertheless, some of these "orphan genes" are high achievers (are just as essential as 'old' genes),,, But where do they come from? With no obvious ancestry, it was as if these genes appeared out of nowhere, but that couldn't be true. Everyone assumed that as we learned more, we would discover what had happened to their families. But we haven't-quite the opposite, in fact.,,, The upshot is that the chances of random mutations turning a bit of junk DNA into a new gene seem infinitesmally small. As the French biologist Francois Jacob wrote 35 years ago, "the probability that a functional protein would appear de novo by random association of amino acids is practically zero".,,, 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. http://ccsb.dfci.harvard.edu/web/export/sites/default/ccsb/publications/papers/2013/All_alone_-_Helen_Pilcher_New_Scientist_Jan_2013.pdf Human Gene Count Tumbles Again - 2008 Excerpt: Scientists on the hunt for typical genes — that is, the ones that encode proteins — have traditionally set their sights on so-called open reading frames, which are long stretches of 300 or more nucleotides, or “letters” of DNA, bookended by genetic start and stop signals.,,,, The researchers considered genes to be valid if and only if similar sequences could be found in other mammals – namely, mouse and dog. Applying this technique to nearly 22,000 genes in the Ensembl gene catalog, the analysis revealed 1,177 “orphan” DNA sequences.,,, the researchers compared the orphan sequences to the DNA of two primate cousins, chimpanzees and macaques. After careful genomic comparisons, the orphan genes were found to be true to their name — they were absent from both primate genomes. http://www.sciencedaily.com/releases/2008/01/080113161406.htm 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 An integrated encyclopedia of DNA elements in the human genome - Sept. 6, 2012 Excerpt: Analysis,,, yielded 57 confidently identified unique peptide sequences in intergenic regions relative to GENCODE annotation. Taken together with evidence of pervasive genome transcription, these data indicate that additional protein-coding genes remain to be found. http://www.nature.com/nature/journal/v489/n7414/full/nature11247.htmlbornagain77_{January 28, 2013
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as to this comment from a 'Darwinian' researcher:
"Although the number of protein coding genes has remained fairly constant throughout metazoan evolution, the number of regulatory DNA elements has increased dramatically."
This sure does sound a whole lot more like 'top down' design than 'bottom up' Darwinian tinkering to me. This following paper found Alternative Splicing ('top down' regulatory) patterns to be 'species specific':
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 ,,,Alternative splicing,,, may contribute to species differences - December 21, 2012 Excerpt: After analyzing vast amounts of genetic data, the researchers found that the same genes are expressed in the same tissue types, such as liver or heart, across mammalian species. However, alternative splicing patterns—which determine the segments of those genes included or excluded—vary from species to species.,,, The results from the alternative splicing pattern comparison were very different. Instead of clustering by tissue, the patterns clustered mostly by species. "Different tissues from the cow look more like the other cow tissues, in terms of splicing, than they do like the corresponding tissue in mouse or rat or rhesus," Burge says. Because splicing patterns are more specific to each species, it appears that splicing may contribute preferentially to differences between those species, Burge says,,, Excerpt of Abstract: To assess tissue-specific transcriptome variation across mammals, we sequenced complementary DNA from nine tissues from four mammals and one bird in biological triplicate, at unprecedented depth. We find that while tissue-specific gene expression programs are largely conserved, alternative splicing is well conserved in only a subset of tissues and is frequently lineage-specific. Thousands of previously unknown, lineage-specific, and conserved alternative exons were identified; http://phys.org/news/2012-12-evolution-alternative-splicing-rna-rewires.html
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