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More Chimp-Human Genome Problems

One of evidences for evolution that has been strongly touted in recent years is the fact that the genomes of the human and chimpanzee are so similar. About 98.4% of the instructions in our genome match the chimp’s. We must share a common ancestor, so goes the argument which doesn’t worry about how humans and chimps could be so different. With a 98.4% match, evolution must be true. That, of course, is not a scientific argument. But leaving that aside, when we look under the hood we actually find that comparisons of the human and chimp genomes contradict evolution.

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30 Responses to More Chimp-Human Genome Problems

  1. Hi all, first time poster. Interesting post Mr Hunter.

    However, increased G+C content is indicative of a region involved in gene expression. Also, the regions flanking these sites promote and control gene expression. So are very much under selection with the gene.

    So these HARs, have increased G+C content, and their promoters have been modified. This all appears to mean they play some type of role. I do not see how this contradicts evolutionary thought.

  2. Very interesting. A couple of years ago, I would have said that the case for human evolution was pretty much ironclad, but I have to say I’m starting to have real doubts, in the light of this new evidence and also a recent article by Dr. Richard Sternberg, entitled Guy Walks Into a Bar and Thinks He’s a Chimpanzee: The Unbearable Lightness of Chimp-Human Genome Similarity , which forced me to reconsider the oft-cited chromosomal evidence for the common ancestry of humans and chimps.

    What I’d really like to see is how the Human Accelerated Regions (HARs) of ancient humans looked: were they like those of modern humans or were they intermediate in form between humans and chimps?

    I know for a fact that Neanderthal DNA has been studied very well – so well that according to this article in The New York Times , Dr. George Church, a leading genome researcher at the Harvard Medical School has said that a Neanderthal could be brought to life with present technology for about $30 million! Did anyone find traces of HARs in Neanderthal DNA?

  3. There is considerable differences between humans. Approximately 1.4 million base pairs per person. Where are those changes located and are they in the HAR’s or not or just randomly scattered throughout the genome?

    Supposedly there was a migration out of Africa roughly 40,000 to 50,000 years ago. By examining the genomes of the people of the various parts of the world one should get a better handle on these HAR’s and how different they are from place to place and how many were intact that long ago. The Neanderthals were supposedly completely eliminated about 25,000 years ago and I am not sure if there ever has been a complete comparison with humans made.

    And the 10 to 15 million base pari differences with humans and chimps seems like a lot of changes to have occurred in 5 million years with a relatively low number of offspring. Not much chance in that time for this many random change to work its way through the populations and become fixed.

    Lots of interesting issues.

  4. 98.4% of genome that scientists managed to align is the same. Significal amount couldn’t be aligned and human and chimp’s genome differ in length.

  5. From:

    http://www.kqed.org/quest/blog.....or-design/

    “Also, when you look at the fusion point, you can see that the DNA isn’t exactly what you would expect if a fusion happened in the last 10,000 or even 100,000 years. The results look more like an event that happened millions of years ago.”

    Anyone know enough to say how many millions? That would be interesting.

  6. Lamarck

    On the page you referenced, if you scroll down, there is a post by Dr. Barry Starr on August 8, 2008 at 10:50 a.m., where he lists two links that support an estimate of somewhere between 740,000 and 3 million years for the timing of the fusion event. In other words, it looks like it happened during the time of Homo erectus or possibly Homo antecessor.

  7. 7

    It’s not just the similarity, but the shared ERVs, transposons, and redundant pseudogenes.

    How is it that we humans have the same mutation that deactivates our vitamin C gene as chimpanzees? The SAME mutation!! How, other than through inheritance, did we acquire the SAME deactivated gene?

  8. Vitamin C refutation here:

    http://truthmatters.info/2007/.....lagiarism/

    excerpt:
    There simply is no evolutionary dead end involved with the lack of a vitamin C enzyme. If there was, evolution might have a case.
    Adam and Eve, Vitamin C, and Pseudogenes
    by Daniel Criswell, Ph.D.

    refutation of Junk DNA here:

    a large sampling of recent studies indicates high level regulatory function is to be found for all sorts of previous “Junk DNA” sequences across the entire spectrum of the human genome. Sequences which were adamantly claimed to be absolute proof for Junk DNA by materialists, as well as adamantly claimed to be absolute proof for common ancestry by them. Yet if Junk DNA sequences show high-level regulatory function, then clearly the Junk DNA sequences can not possibly be considered “recent evolutionary add-ons”, and as such, nor can they be construed as proof for common ancestry.

    These following sites are excellent and have over one hundred peer-reviewed papers refuting every single class of Junk DNA that has been put forth by materialists:

    Endogenous Retroviruses (ERVs) – Page up for Pseudo-genes refutation
    http://www.detectingdesign.com.....Endogenous

    Endogenous Retroviruses (ERVS) A Case for Common Descent or A Case for Incorrect Presupposition?
    http://www.whoisyourcreator.co.....ruses.html

    How Scientific Evidence is Changing the Tide of the Evolution vs. Intelligent Design Debate by Wade Schauer:
    List Of “Junk DNA discussed:
    Tandem Repeats, Transposons/Retrotransposons, SINE/Alu Sequences, LINES, Endogenous Retroviruses (ERVs) and LTR retrotransposons, Pseudogenes, C-Value Enigma, “Junk DNA” becomes “The Transcriptome”, “Junk DNA – the biggest mistake in the history of biology”, EVOLUTIONARY CONSERVATION, Human Accelerated Regions (HARs),
    ….What can we conclude from the evidence presented in this essay:
    · Every type of “Junk DNA” presented by pro-evolution websites has been found to have functional roles in organisms, which severely undermines the “shared errors” argument;
    http://www.geocities.com/wade_.....g_Tide.pdf

    On the roles of repetitive DNA elements in the context of a unified genomic-epigenetic system: – Sternberg R.
    It is argued throughout that a new conceptual framework is needed for understanding the roles of repetitive DNA in genomic/epigenetic systems, and that neo-Darwinian “narratives” have been the primary obstacle to elucidating the effects of these enigmatic components of chromosomes.

    Here are a few more recent papers that have revealed high-level regulatory function for large sections of DNA sequences of what were once considered useless Junk DNA sequences by the materialist.

    Retroviral promoters in the human genome, Bioinformatics
    Our analysis revealed that retroviral sequences in the human genome encode tens-of-thousands of active promoters; transcribed ERV sequences correspond to 1.16% of the human genome sequence and PET tags that capture transcripts initiated from ERVs cover 22.4% of the genome. These data suggest that ERVs may regulate human transcription on a large scale. (Andrew B. Conley, Jittima Piriyapongsa and I. King Jordan, Vol. 24(14):1563–1567 (2008).)
    http://www.ncbi.nlm.nih.gov/pubmed/18535086

    Nature Paper Shows “Junk-RNA” Going the Same Direction as “Junk-DNA”
    “Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals, February 2009″
    .. rather than being “transcriptional noise,” over 95% of the non-coding RNAs studied in the paper show “clear evolutionary conservation.”

    The regulated retrotransposon transcriptome of mammalian cells April 2009 : Geoffrey J Faulkner:
    We conclude that retrotransposon transcription has a key influence upon the transcriptional output of the mammalian genome.
    http://www.nature.com/ng/journ.....g.368.html

    ‘Junk’ DNA Has Important Role, Researchers Find: 21 May 2009:
    Excerpt: DNA sequences from regions of what had been viewed as the “dispensable genome” are actually performing functions that are central for the organism. They have concluded that the genes spur an almost acrobatic rearrangement of the entire genome that is necessary for the organism to grow.
    http://www.sciencedaily.com/re.....140408.htm

    Saved By Junk DNA: 30 May 2009
    One commonly known example of such ‘junk DNA’ are the so-called tandem repeats, short stretches of DNA that are repeated head-to-tail. “At first sight, it may seem unlikely that this stutter-DNA has any biological function,” says Marcelo Vinces, one of the lead authors on the paper.

    Unstable repeats: The international team of scientists found that stretches of tandem repeats influence the activity of neighboring genes. The repeats determine how tightly the local DNA is wrapped around specific proteins called ‘nucleosomes’, and this packaging structure dictates to what extent genes can be activated.

    “Junk DNA” is found to have purpose in an astonishing way in this following paper:

    Shoddy Engineering or Intelligent Design? Case of the Mouse’s Eye – April 2009
    Excerpt: –Why the elaborate repositioning of so much “junk” DNA in the rod cells of nocturnal mammals? The answer is optics… The (entire) nuclear genome is thus transformed into an optical device that is designed to assist in the capturing of photons. This chromatin-based convex (focusing) lens is so well constructed that it still works when lattices of rod cells are made to be disordered. Normal cell nuclei actually scatter light. — So the next time someone tells you that it “strains credulity” to think that more than a few pieces of “junk DNA” could be functional in the cell – remind them of the rod cell nuclei of the humble mouse.

    Astonishing DNA complexity demolishes neo-Darwinism – Alex Williams:
    Excerpt: DNA information is overlapping-multi-layered and multi-dimensional; it reads both backwards and forwards; and the ‘junk’ is far more functional than the protein code, so there is no fossilized history of evolution…All the vast amount of meta-information in the human genome only has meaning when applied to the problem of using the human genome to make, maintain and reproduce human beings.
    http://creation.com/images/pdf.....11-117.pdf

  9. Refutation of Chimp human similarity similarity here:

    For prime example of the flimsy “similarity evidence” used by materialists to try to make their case for evolution, most materialists are adamant Darwinian evolution is proven true when we look at the supposed 98.8% genetic similarity between chimps and man. Though suggestive, the gene similarity, even if true, is not nearly good enough to be considered conclusive scientific proof. Primarily this “lack of conclusiveness” is due to concerns with the second law of thermodynamics and with the Law of Conservation of Information. But of more pressing concern, body plans are not even encoded in the DNA code in the first place. This inability of body plans to be reduced directly to the DNA code is clearly shown by Cortical Inheritance.

    Cortical Inheritance: The Crushing Critique Against Genetic Reductionism – Arthur Jones – video
    Part 1 http://www.youtube.com/watch?v=5JzQ8ingdNY
    Part 2 http://www.youtube.com/watch?v=o1bAX93zQ5o

    This inability for the DNA code to account for body plans is also clearly shown by extensive mutation studies to the DNA of different organisms which show “exceedingly rare” major morphological effects from mutations to the DNA code.

    Hopeful monsters,’ transposons, and the Metazoan radiation:
    Excerpt: Viable mutations with major morphological or physiological effects are exceedingly rare and usually infertile; the chance of two identical rare mutant individuals arising in sufficient propinquity to produce offspring seems too small to consider as a significant evolutionary event. These problems of viable “hopeful monsters” render these explanations untenable.
    Paleobiologists Douglas Erwin and James Valentine

    This includes the highly touted four-winged fruit fly mutations.

    …Advantageous anatomical mutations are never observed. The four-winged fruit fly is a case in point: The second set of wings lacks flight muscles, so the useless appendages interfere with flying and mating, and the mutant fly cannot survive long outside the laboratory. Similar mutations in other genes also produce various anatomical deformations, but they are harmful, too. In 1963, Harvard evolutionary biologist Ernst Mayr wrote that the resulting mutants “are such evident freaks that these monsters can be designated only as ‘hopeless.’ They are so utterly unbalanced that they would not have the slightest chance of escaping elimination through natural selection.” – Jonathan Wells

    Darwin’s Theory – Fruit Flies and Morphology – video
    http://www.youtube.com/watch?v=hZJTIwRY0bs

    If all that wasn’t enough, the Human Genome Project really put the last nail in the coffin for “Genetic Reductionism”:

    DNA: The Alphabet of Life – David Klinghoffer
    Excerpt: But all this is trivial compared to the largely unheralded insight gained from the Human Genome Project, completed in 2003. The insight is disturbing. It is that while DNA codes for the cell’s building blocks, the information needed to build the rest of the creature is seemingly, in large measure, absent. ,,,The physically encoded information to form that mouse, as opposed to that fly, isn’t there. Instead, “It is as if the ‘idea’ of the fly (or any other organism) must somehow permeate the genome that gives rise to it.”
    http://www.evolutionnews.org/2....._life.html

    Thus the 98.8% similarity derived from the DNA code, to the body plans of chimps and man, is purely imaginary, since it is clearly shown that the overriding “architectural plan” of the body is not even encoded in the DNA in the first place. Of more clarity though, this “98.8% similarity evidence” is derived by materialists from a very biased methodology of presuming that the 1.5% of the genome, which directly codes for proteins, has complete precedence of consideration over the other remaining 98.5% of the genome which does not directly code for proteins. Yet even when considering just this 1.5% of the genome that codes for proteins, we find that the proteins, which are directly coded by that 1.5% of the genome, are shown to differ by a huge 80% difference between chimps and man.

    Chimps are not like humans – May 2004
    Excerpt: the International Chimpanzee Chromosome 22 Consortium reports that 83% of chimpanzee chromosome 22 proteins are different from their human counterparts,,, The results reported this week showed that “83% of the genes have changed between the human and the chimpanzee—only 17% are identical—so that means that the impression that comes from the 1.2% [sequence] difference is [misleading]. In the case of protein structures, it has a big effect,” Sakaki said.
    http://cmbi.bjmu.edu.cn/news/0405/119.htm

    Eighty percent of proteins are different between humans and chimpanzees; Gene; Volume 346, 14 February 2005:
    http://www.ncbi.nlm.nih.gov/pubmed/15716009

    On top of that huge 80% difference in proteins, the oft quoted 98.8% DNA similarity is not even rigorously true in the first place. Just considering this 1.5% of the genome, other recent comparisons of the protein coding genes, between chimps and man, have yielded a similarity of only 96%. Whereas, the December 2006 issue of PLoS ONE reported that human and chimpanzee gene copy numbers differ by 6.4%, which gives a similarity of only 93.6% (Hahn). Even more realistically, to how we actually should be looking at the genomes from a investigative starting point, Dr. Hugh Ross states the similarity is closer to 85% to 90% when taking into account the chimp genome is about 12% larger than the human genome. A recent, more accurate, human/chimp genome comparison study, by Richard Buggs in 2008, has found when he rigorously compared the recently completed sequences in the genomes of chimpanzees to the genomes of humans side by side, the true genome similarity between chimps and man fell to slightly below 70%! Why is this study ignored since the ENCODE study has now implicated 100% high level functionality across the entire human genome? Finding compelling evidence that implicates 100% high level functionality across the entire genome clearly shows the similarity is not to be limited to the very biased “only 1.5% of the genome” studies of materialists.

    Chimpanzee?
    10-10-2008 – Dr Richard Buggs – research geneticist at the University of Florida
    …Therefore the total similarity of the genomes could be below 70%.
    http://www.refdag.nl/artikel/1.....anzee.html

    More Chimp-Human Genome Problems – Cornelius Hunter
    Excerpt: Even more interesting, at these locations the chimp’s genome is quite similar to other primates–it is the human that differs from the rest, not the chimp. (human accelerated regions (HARs).

    As mentioned previously, the chimpanzee is found to have a 12% larger genome than humans. Thus, at first glance it would seem the chimpanzee is more evolved than us, but this discrepancy is no anomaly of just chimps/humans. This disparity of genome sizes is found throughout life. There is no logical “evolutionary” progression to be found for the amount of DNA in less complex animals to the DNA found in more complex animals. In fact the genome sizes are known to vary widely between Kinds/Species and this mystery is known as the c-value enigma:

    C-value enigma
    Excerpt: it was soon found that C-values (genome sizes) vary enormously among species and that this bears no relationship to the presumed number of genes (as reflected by the complexity of the organism). For example, the cells of some salamanders may contain 40 times more DNA than those of humans. Given that C-values were assumed to be constant because DNA is the stuff of genes, and yet bore no relationship to presumed gene number, this was understandably considered paradoxical;

    This following paper reiterates the biased methodology of establishing 98.8% similarity, between chimps and man, used by materialists:

    The Unbearable Lightness of Chimp-Human Genome Similarity
    excerpt: One can seriously call into question the statement that human and chimp genomes are 99% identical. For one thing, it has been noted in the literature that the exact degree of identity between the two genomes is as yet unknown (Cohen, J., 2007. “Relative differences: The myth of 1%,” Science 316: 1836.). Part of the reason for this is if one decides to take into account the plethora of species-specific DNA insertions and deletions (“indels”) that are present along any segment compared between chimp and human, the percentage of identity drops. Another reason is that duplications, inversions, translocations, and transpositions at all scales uniquely characterize the two genome sequences — these have to be untangled before aligning the sequences in order to measure their similarity. Also, the 99% identity figure is often derived from protein-coding regions that only comprise about 1.5% of the two genomes. Many mammalian protein-coding regions are highly conserved, however. We also have to consider that a detailed comparison of certain “heterochromatic” chromosome regions between chimps and humans has yet to be made. In short, the figure of identity that one wants to use is dependent on various methodological factors.

    As well, there are at least 50 to 100 genes which are completely unique to humans:

    Among the approximately 23,000 genes found in human DNA there may be,, 50 to 100 that have no counterparts in other species.
    http://mednews.wustl.edu/news/.....11349.html

  10. bornagain77,

    http://truthmatters.info/2007/.....lagiarism/

    Are you familiar with Dave Hawkins? Anyway, let me ask, what sort of evidence for common ancestry of chimps and humans would you accept? I’ll also note that Dr. Behe accepts common ancestry of chimps and humans, in part because of the vitamin C pseudogene evidence.

  11. 11

    bornagain77,

    The mutation that deactivates our vitamin C genes do not have to be identical. Over time, due to other mutations, the gene would change even further.

    What we see is that the vitamin C gene mutation is most similar to chimpanzees, then other great apes, and finally the other primates, exactly as predicted by the phylogenetic primate tree.

    link

  12. Believe such shoddy conjecture if you must, you will anyway I am afraid,,, but the evidence against the vitamin C conjecture is solid,,,and is moot as far as proving evolution because number one it is a loss of functional information, not a gain, and two we have a 100% poly-functionality genome (ENCODE) equaling a severely poly constrained genome (Sanford).

    Astonishing DNA complexity demolishes neo-Darwinism:
    DNA information is overlapping-multi-layered and
    multi-dimensional; it reads both backwards and forwards; and the ‘junk’ is far more functional than the protein code, so there is no fossilized history of evolution. No human engineer has ever even imagined, let alone designed an information storage device anything like it. Moreover, the vast majority of its content is metainformation— information about how to use information. Meta-information cannot arise by chance because it only makes sense in context of the information it relates to.
    http://creation.com/images/pdf.....11-117.pdf

    Psalm 139:16
    and in thy book all my members were written, which in continuance were fashioned, when as yet there was none of them.

    The point is you guys are are grasping for very dubious evidence in the face of solid evidence to the contrary,,,what you guys need to do if you were truly concerned about finding the truth of the matter is to try to find instances where functional complexity was increased instead of supposedly lost.

    Professional evolutionary biologists are hard-pressed to cite even one clear-cut example of evolution through a beneficial mutation to the DNA of humans which would violate the principle of genetic entropy. Although a materialist may try to claim the lactase persistence mutation as a lonely example of a “truly” beneficial mutation in humans, lactase persistence is actually a loss of a instruction in the genome to turn the lactase enzyme off, so the mutation clearly does not violate Genetic Entropy. Yet at the same time, the evidence for the detrimental nature of mutations in humans is overwhelming for doctors have already cited over 3500 mutational disorders (Dr. Gary Parker).

    “Mutations” by Dr. Gary Parker
    Excerpt: human beings are now subject to over 3500 mutational disorders.
    http://www.answersingenesis.or.....ations.asp

    Thus if you want to be “scientific” you will address this clear information problem instead of try to “get over” with such hoodwinked empirics for vitamin C.

    etc…etc…etc…

  13. bornagain77,

    Believe such shoddy conjecture if you must, you will anyway I am afraid …

    This reply wasn’t directed toward me, I suspect, but I just want to reiterate that while you speak of “shoddy conjecture[s]“, you quote Dave Hawkins of all people to support your case. He’s a YEC who believes Noah’s Flood was caused by the “fountains of the deep” exploding with the force of 300 trillion atomic bombs, hurling debris into orbit around the sun, thereby creating the asteroid belt. The Ark and its occupants were unharmed, naturally. Believe me, he’s not a person you want on your side in any debate.

  14. yakky,,Though I am far from being in agreement with YECers,,,I got far more respect for YECers than I do evolutionists as far as the science of molecular biology is concerned….

  15. bornagain77,

    yakky,,Though I am far from being in agreement with YECers,,,I got far more respect for YECers than I do evolutionists as far as the science of molecular biology is concerned….

    That’s fine, and of course this isn’t all about authority. But do you really trust Dave Hawkins over Michael Behe on this matter?

  16. Yakky,
    I trust what I know from foundational laws of physics, namely Conservation of Information and Genetic Entropy….

  17. bornagain,

    I trust what I know from foundational laws of physics, namely Conservation of Information and Genetic Entropy….

    I don’t think those are considered foundational laws of physics by physicists. If you can provide a citation, then I’d be happy to change my mind.

    But what sort of evidence for common ancestry would you find convincing?

  18. yakky,
    If you can provide a citation, then I’d be happy to change my mind.

    That I highly doubt….

  19. 19

    bornagain77,

    Common descent predicts that we will find such things as shared molecular vestiges among related organisms.

    It PREDICTS that organisms closely related will share pseudogenes that are very similar, and organisms that are less closely related will share pseudogenes that are less similar, etc, on down the phylogenetic tree.

    This is exactly what we see with the vitamin C gene, regardless of your attempts to bring in red herrings like information increase/decrease.

    While you can always say that a designer just made it like that, a creation model doesn’t PREDICT such a thing happening. It’s more parsimonious to attribute it to common descent.

  20. Well Singblue,
    Let’s pretend you will follow the evidence, and dismantle your deception one piece at a time.

    you state:

    “It PREDICTS that organisms closely related will share pseudogenes that are very similar, and organisms that are less closely related will share pseudogenes that are less similar, etc, on down the phylogenetic tree.”

    yet it is now known you “tree” is annihilated :

    Why Darwin was wrong about the (genetic) tree of life: – 21 January 2009
    excerpt: Syvanen recently compared 2000 genes that are common to humans, frogs, sea squirts, sea urchins, fruit flies and nematodes. In theory, he should have been able to use the gene sequences to construct an evolutionary tree showing the relationships between the six animals. He failed. The problem was that different genes told contradictory evolutionary stories. This was especially true of sea-squirt genes. Conventionally, sea squirts – also known as tunicates – are lumped together with frogs, humans and other vertebrates in the phylum Chordata, but the genes were sending mixed signals. Some genes did indeed cluster within the chordates, but others indicated that tunicates should be placed with sea urchins, which aren’t chordates. “Roughly 50 per cent of its genes have one evolutionary history and 50 per cent another,” Syvanen says. ….”We’ve just annihilated the tree of life. It’s not a tree any more, it’s a different topology entirely,” says Syvanen. “What would Darwin have made of that?”
    http://www.newscientist.com/ar.....-life.html

    I would like to point out that this, “annihilation” of Darwin’s genetic tree of life, article came out on the very day that Dr. Hillis, a self-proclaimed “world leading expert” on the genetic tree of life, testified before the Texas State Board Of Education that the genetic tree of life overwhelmingly confirmed gradual Darwinian evolution. One could almost argue it was “Intelligently Designed” for him to exposed as a fraud on that particular day of his testimony instead of just any other day of the year.

    As well the fossil evidence is nowhere as smooth as you imagine it to be:

    “Fossil evidence of human evolutionary history is fragmentary and open to various interpretations. Fossil evidence of chimpanzee evolution is absent altogether”. Evolutionist Henry Gee, Nature 2001
    http://www.nature.com/nature/j.....131a0.html

    “The australopithecine (Lucy) skull is in fact so overwhelmingly simian as opposed to human that the contrary proposition could be equated to an assertion that black is white.” Lord Solly Zuckerman – Chief scientific advisor to British government and leading zoologist

    Evolution of the Genus Homo – Annual Review of Earth and Planetary Sciences – Tattersall, Schwartz, May 2009
    Excerpt: “Definition of the genus Homo is almost as fraught as the definition of Homo sapiens. We look at the evidence for “early Homo,” finding little morphological basis for extending our genus to any of the 2.5–1.6-myr-old fossil forms assigned to “early Homo” or Homo habilis/rudolfensis.”
    http://arjournals.annualreview.....208.100202

    Man is indeed as unique, as different from all other animals, as had been traditionally claimed by theologians and philosophers.
    Evolutionist Ernst Mayr http://www.y-origins.com/index.php?p=home_more4

    “Something extraordinary, if totally fortuitous, happened with the birth of our species….Homo sapiens is as distinctive an entity as exists on the face of the Earth, and should be dignified as such instead of being adulterated with every reasonably large-brained hominid fossil that happened to come along.” Anthropologist Ian Tattersall (curator at the American Museum of Natural History)

  21. You go on about the vitamin c gene and pseudo genes as if this will make up for your glaring deficiencies with more foundational evidence (such as the “information generation problem” you had the audacity to call a red herring).

    But what do you really have?

    Excerpt: Stating that only the last enzyme is missing for the pathway to convert glucose to vitamin C might imply to the untrained individual that there is a biochemical pathway that leads to a dead end. Actually, the biochemical pathway that leads to the synthesis of vitamin C in rats also leads to the formation of five-carbon sugars in the pentose phosphate pathway present in virtually all animals (Linster and Van Schaftingen 2007). There are several metabolic intermediates in this pathway illustrating that these substances can be used as precursors for many compounds in the cell. In the pentose phosphate pathway, five-carbon sugars are made from glucose (a six-carbon sugar) to be used in the synthesis of DNA, RNA, and many energy producing substances such as ATP and NADPH (Garrett 1999). Animals that synthesize vitamin C can use both pathways illustrated in the simplified diagram below. Humans and the other animals “less fortunate” than rats only use the pentose phosphate pathway.

    There is no dead end or wasted metabolic intermediates, and there is no need to have the enzyme to make vitamin C since humans are able to get all of the vitamin C they need from food substances.
    http://truthmatters.info/2007/.....lagiarism/

    Thus to call it purely a “Junk” pseudogene that has ceased to produce vitamin c, and is lay down proof of common decent seems to be very premature on your part as the “Junk” psuedo gene is in fact shown to be polyfunctional:

    But let’s look at recent work on the supposed JUNK of pseudogenes:

    In evolutionary conserved regions, 90% of pseudogenes appear to be under regulation. Note also that
    the Panda’s Thumb article assumes that Methylation means “inactivity”/non-function, while these
    researchers conclude it implies regulatory function.
    http://ec.europa.eu/research/h.....21_en.html
    They discovered that regions called evolutionary conserved regions (ECRs), lying distant from genes, out in
    the ‘junk’ DNA, had high concentrations of methylation. This may indicate that these regions have an
    undiscovered role to play in gene or chromosome activity, according to the scientists.
    In addition, analysis of methylation led the team to portions of DNA previous thought to be relatively inactive.
    Some portions of DNA, known as pseudogenes, appear to have lost function or their exact function is unknown
    because they have not yet been experimentally studied. Researchers found that these regions were
    approximately 90 percent methylated, leading them to suspect that methylation might contribute to the
    inactivity of such genes.
    9
    Functional Small nucleolar RNAs (snoRNA) were previously mistaken as pseudogenes
    http://genetics.plosjournals.o.....en.0020205
    Although four examples of Type-1 retroposons were previously reported [25,43], types 2 and 3 are
    characterized here for the first time. Several Type-3 snoRTs originating from ribosomal protein genes were
    previously annotated as processed pseudogenes, but their intronic parts (snoRNA sequence and downstream
    intron) were overlooked since the pseudogenes were identified by alignment of cDNA or peptide sequences
    with genomic sequences
    The NANOG Pseudogene family is touted by evolutionists as an example of common descent between
    Humans & Chimps. Meanwhile research has shown that the NANOG Pseudogenes 1 & 8 appear to
    have regulatory roles (for starters)
    http://stemcells.alphamedpress...../23/8/1035
    The most effective short double-stranded RNA corresponded to a sequence shared by NANOG and the
    duplication pseudogene, NANOGP1. This would suggest that NANOGP1 transcript, despite not being
    translated into a protein, would be downregulated as result of the RNAi approach.
    http://content.febsjournal.org.....273/8/1723
    The expression of NANOGP8 in cancer cell lines and cancer tissues suggests that NANOGP8 may play
    important roles in tumorigenesis. This work not only has potential significance in stem cell and cancer
    research, but it also raises the possibility that some of the human pseudogenes may have regulatory functions.

  22. more on pseudo genes:

    Alpha globin pseudogene discovered to be functional gene
    http://www.bloodjournal.org/cg.....0948v1.pdf
    Surprisingly, we also identified transcription from the genomic region previously thought to encode the
    pseudo-alpha2 gene. The source of that transcription is characterized in this report as a previously
    unrecognized globin gene.
    Unprocessed KLK pseudogene expressed abundantly in prostate tissues
    http://www3.interscience.wiley...../112492090
    KLK31P is a novel androgen regulated and transcribed pseudogene of kallikreins that may play a role in
    prostate carcinogenesis or maintenance… KLK31P is expressed abundantly in prostate tissues and is
    androgen regulated. KLK31P is expressed at lower levels in localized and metastatic prostate cancer cells
    than in normal prostate cells.
    Pseudogene inhibits tumor growth – may have other roles
    http://www.ncbi.nlm.nih.gov/en.....dopt=Abstr
    act
    Based on our findings, PsiCx43 joins and enlarges the thus far restricted group of functionally transcribed and
    translated pseudogenes.
    Two examples of Micro-RNA arising from within processed pseudogenes
    http://jhered.oxfordjournals.o.....t/97/2/186
    A survey of the genomic context of more than 300 human miRNA loci revealed that two primate-specific
    miRNAs, miR-220 and miR-492, each lie within a processed pseudogene.
    41% of pseudogenes have match to small RNAs, while only 1 in 6 genes do…
    http://forest.mtu.edu/faculty/....._sRNAs.pdf
    Oct4 pseudogene – functional relevance and indicative of epigenetic regulation
    http://www.jbc.org/cgi/content/full/280/8/6265
    Through analysis of the mouse genome, we also found that an Oct4 pseudogene was located in the same locus
    as Nanog, Stella, and GDF3 on chromosome 6. Moreover, the relative positional order of these genes was
    conserved between the mouse and human genomes. By BLASTing the EST data base we found that this mouse
    pseudogene is likely transcribed, as an exact sequence hit was generated (data not shown). This suggests that
    the mouse oct4 pseudogene, which colocalizes with Nanog, Stella, and GDF3 is transcriptionally functional.

    etc…etc…etc…

    thus you are completely undermined in your deception here SingBlue…Or do you want to insist that we continue to call these elements “Junk DNA”, if so you are not practicing science and will reveal yourself for a dogmatic atheist.

  23. Now SingBlue do you mind citing just one example of genetic entropy of the original parent species being violated by a sub-species? I know you called this a red herring,,,and you probably feel it is beneath you to actually prove the generation of functional information that is greater than what was present in the parent species,and thus prove evolution,but please do humor me on this point being as you think you know so much more than I, plus have such brazenness as to apparently deny the existence of Almighty God and forsake the salvation He has laid out for you through Christ…(Myself,,,,I can’t see as to how you could find this confidence of disbelief when all evidence I examine screams of the Creator and makes me cling all the more fiercely to the reconciliation He has freely offered through Christ!) Be that as it may,, please do lay out your case once again for such audacity as to play God of no consequence for you to consider…

  24. 24

    thus you are completely undermined in your deception here SingBlue…Or do you want to insist that we continue to call these elements “Junk DNA”, if so you are not practicing science and will reveal yourself for a dogmatic atheist.

    Holy moly you’ve gone off track.

    Here is the argument: mutation that makes our vitamin C gene no longer make vitamin C is almost exactly the same mutation seen in chimpanzees, slightly less so than that seen in gorillas, and slightly less so in that seen in the other primates. As predicted by common descent, we are most closely related to chimps, less so to gorillas, and even less so to the other primates.

    In comparison, the mutation that makes the vitamin C gene no longer make vitamin C in guinea pigs is a completely different mutation. Consistent with common descent, which does not predict a recent common ancestor with humans and guinea pigs.

    You answered:

    - “New Scientist says the Darwin tree is wrong”

    - yes, the idea of a single tree is being disputed; there is evidence of several trees, lateral gene transfer, etc. but family and genus phylogenetics has not changed. the theory still says humans are part of the primate branch. and regardless, this is irrelevant to the point: that humans share a vitamin C mutation with chimps, exactly as primate phylogeny predicts.

    - “the vitamin C gene is not junk” – never said it was, and it’s irrelevant to this particular argument regardless.

    - “it’s an information decrease, not increase”
    - also irrelevant to this particular argument – it’s a red herring because instead of answering this particular argument you go willy nilly into general arguments against evolution – it does not answer how humans and chimpanzees ended up with the same mutation of vitamin C genes

    - “quotes from biologists about how humans are special, Lucy is really an ape, human evolution isn’t well understood, etc etc etc”
    - more irrelevance to this particular argument. what the hell does Lucy have to do with how humans and chimpanzees acquired the same mutation of their vitamin C genes?

    So the question remains: how did we acquire the same mutated vitamin C gene as chimps, which is less similar to that of gorillas, which is less similar to that of lesser primates, exactly as predicted by primate phylogeny, without the mechanism of inheritance?

  25. SingBlue,
    You presupposed non-functionality and it is shown the supposed pseudogene of Vitamin C is polyfunctional and of an essential base nature to life(Actually, the biochemical pathway that leads to the synthesis of vitamin C in rats also leads to the formation of five-carbon sugars in the pentose phosphate pathway present in virtually all animals (Linster and Van Schaftingen 2007).), thus undermining your necessary base conjecture of a functionless gene..Thus you are falsified whether you admit it or not since it shown to have a foundational level of function for life..But this is all beside the point as you have yet to address why should we presuppose common descent to be true when evolution has not even demonstrated one instance of primary speciation…. You have put the cart way before the horse in your science and are damned determined to let your ideology drive your science ,,,but I am not going to play your stupid games of deception and will insist you show the generation of functional information that is greater than what is present in the parent species genome,,,else wise you are just an ideologue trying to justify his atheism in my book! I shall not waste my time with your games!

  26. 26

    …thus undermining your necessary base conjecture of a functionless gene

    You just can’t seem to stick to the argument at hand.

    Whether the gene is functional or not is not a necessary part of the argument.

    Again: the mutation in the vitamin C gene is the same mutation in the entire primate family, with more similarity being found among predicted closely related primates and less similarity being found among more distant predicted relatives.

    …show the generation of functional information that is greater than what is present in the parent species genome…

    That’s a whole other argument. I was only responding to the incorrect statement that “evolutionists think humans and chimps are related because of the 98% similarity in their genomes.”

    Evolutionists think we are related because of that, AND the shared mutations, AND the shared ERVs, AND the shared transposons, all of which can ONLY be shared through inheritance.

    …else wise you are just an ideologue trying to justify his atheism…

    How do you know I’m atheist?

  27. SingBlue,
    you have presupposed that the function is completely known for the gene when I have showed, albeit tentatively, that a more base function is to be found, you presuppose a mutation in the same spot but I have clearly shown the biased methodology used by materialist to arrive at such similarity. i.e. you have presupposed the question to be true in order to prove the question at hand! This is crap science to put it mildly. You totally have ignored the 100% functionality of the Genome which precludes novel information generation just so as to preserve you dubious conjecture of common ancestry…more crap science on your part…That the similarity between chimps and man is actually below 70% when taking into account the 100% poly-functionality revealed by ENCODE is of no matter to you since it completely undermines your unfounded belief…more crap science by you…for you then to pretend you don’t see this and pretend is does not reveal your atheistic bias is an insult to reason…I will not play your stupid games and will continue to call on you to produce evidence of information generation,,,elsewise your are just ignoring what really matters in order to protect what is false, as I said it is just crap science by you!

  28. Evolution of the appendix: A biological ‘remnant’ no more

    The lowly appendix, long-regarded as a useless evolutionary artifact, won newfound respect two years ago when researchers at Duke University Medical Center proposed that it actually serves a critical function. The appendix, they said, is a safe haven where good bacteria could hang out until they were needed to repopulate the gut after a nasty case of diarrhea, for example.

    Writing in the Journal of Evolutionary Biology, Duke scientists and collaborators from the University of Arizona and Arizona State University conclude that Charles Darwin was wrong: The appendix is a whole lot more than an evolutionary remnant. Not only does it appear in nature much more frequently than previously acknowledged, but it has been around much longer than anyone had suspected.

    Check it out. Yet another example of how the scavenger hunt for vestigial organs is harmful to medical science.

  29. Which goes to prove that science is not static… How long since Dawkins created “Weasel”?

  30. SingBlueSilver:

    Evolutionists think we are related because of that, AND the shared mutations, AND the shared ERVs, AND the shared transposons, all of which can ONLY be shared through inheritance.

    How do you know that?

    IOW how can that premise be tested?

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