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We Can Now Obtain Erroneous Results Faster

A new method for computing evolutionary trees may revolutionize evolutionary biology. That’s good because evolutionary biology needs some revolutionizing. So far its fundamental predictions have consistently turned out to be false. Indeed, at evolutionary biology’s very core, the idea of an evolutionary tree is problematic given the data, and even some evolutionists are suggesting the “tree thinking” may not be useful. But the new research isn’t likely to help on that score. What the research does enable is the creation of erroneous results at a much faster pace.

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44 Responses to We Can Now Obtain Erroneous Results Faster

  1. Cornelius Hunter writes:

    The idea that the species evolved according to common descent, along some sort of evolutionary tree, is not motivated by the evidence.

    Cornelius,

    That statement is ludicrous. As I commented in another thread:

    Phinehas asked:

    I’ve often wondered, however, whether the inference to common descent has ever been subjected to the same mathematical rigor as the design inference.

    It’s been demonstrated far more rigorously than any design inference. As [Douglas] Theobald explains:

    The degree of phylogenetic congruence between these independent data sets is nothing short of incredible… So, how well do phylogenetic trees from morphological studies match the trees made from independent molecular studies? There are over 10^38 different possible ways to arrange the 30 major taxa represented in Figure 1 into a phylogenetic tree (see Table 1.3.1; Felsenstein 1982; Li 1997, p. 102). In spite of these odds, the relationships given in Figure 1, as determined from morphological characters, are completely congruent with the relationships determined independently from cytochrome c molecular studies (for consensus phylogenies from pre-molecular studies… Speaking quantitatively, independent morphological and molecular measurements such as these have determined the standard phylogenetic tree, as shown in Figure 1, to better than 38 decimal places.

  2. 2
    Cornelius Hunter

    mereologist:

    That statement is ludicrous. As I commented in another thread:

    You must not be familiar with the research. If you are looking for statements that are “ludicrous” I suggest actually looking at the research you cite. One could just as easily make such absurd claims for geocentrism.

    The first question one might ask is “How do they obtain 38 decimal places; what data filtering is used and what assumptions are crucial to that result?”

  3. Cornelius Hunter:

    Nor can they be due to a similar environment…

    Why not? They are, presumably, environments with light?

  4. The first question one might ask is “How do they obtain 38 decimal places; what data filtering is used and what assumptions are crucial to that result?”

    Cornelius,

    In the future, you would do well to understand how such research is done before presuming to criticize it as “not motivated by the evidence”.

    The 38 decimal places come from the fact that the 30 taxa can be arranged into more than 10^38 possible trees, yet independent morphological and molecular studies converge on the same tree. This is stupendous evidence for common descent. The odds of it happening by chance are less than 1 in 10^38; thus we say that the standard phylogenetic tree is known to an accuracy of better than 38 decimal places.

    You and others who dismiss common descent should ponder this long and hard. It implies that either common descent is true, or the designer has made it appear, overwhelmingly, to be true. Either way, you you have to ignore the evidence — all 38 decimal places worth — to conclude that common descent is false.

    I should add that ID supporters who accept common descent are not off the hook either. If the designer uses common descent but either front-loads information or intervenes and adds it during the development of life, then there is no reason for the molecular data to conform to the same standard tree as the morphological data. The designer could have chosen one of the trillions of trillions of schemes that would have caused a mismatch between the two.

    This means that the dilemma I posed above, slightly revised, applies to all ID supporters, including those who accept common descent:

    Either undirected evolution is true, or the designer has made it appear, overwhelmingly, to be true. Either way, you you have to ignore the evidence — all 38 decimal places’ worth — to conclude that ID is correct.

    It’s surprising to me that so few ID supporters recognize the magnitude of the problem. When ID critics talk about “overwhelming evidence”, they aren’t kidding!

  5. I’ll mention the Phylogenetic Tree of Mixed Drinks again.

    spaghettilogic.org seems to be gone now, but the chart and some details are still available elsewhere:

    http://blog.makezine.com/archi....._tree.html)

  6. mereologist,

    The 38 decimal places come from the fact that the 30 taxa can be arranged into more than 10^38 possible trees, yet independent morphological and molecular studies converge on the same tree.

    Surely there must be a large number of different ways to derive these trees, correct? Isn’t there a danger of choosing whichever scheme confirms your hypothesis? And how do we know these morphological and molecular methods are independent? As I’m sure you’re aware, those of us in the ID community are always on the lookout for crappy probability arguments.

  7. anonym,

    The “Phylogenetic Tree of Mixed Drinks” is an amusing diversion, but it has no relevance to the question of whether biological taxonomic trees are accurate.

    You seem to think that it is somehow ridiculous for PHYLIP to produce an answer when given the ingredient lists for mixed drinks, but what you may not realize is that programs like PHYLIP will always give an answer, even if the data they are operating on is garbage. That’s how they are supposed to work, because they are looking for the phylogenetic tree that best matches the data. Even if the data were completely random, some trees would match the data better than others. PHYLIP’s job is to find the best match, period.

    So far from being ridiculous, the fact that PHYLIP produced a tree of mixed drinks is absolutely expected.

    The reason that biologists accept the standard phylogenetic tree is not merely because programs like PHYLIP produce an answer; it’s because they produce matching answers even when operating on independent data sets.

    As Theobald explains, the tree generated from morphological data matches the tree generated from cytochrome c data to an accuracy of better than 38 decimal places. It is the precision of this match that demonstrates the truth of common descent, not the mere fact that the analysis produces an answer.

  8. mereologist,

    Are you referring to tree alignment on 18s rRNA or perhaps 28s rRNA? From Jonathan Well’s book:

    Obviously, Futuyama’s claim that molecular phylogenies tend to support traditional morphological phylogenies is not true in this case. IN fact, results from 28s rRNA (a larger molecule also found in ribosomes) conflict with results from 18s rRNA. Even worse, 18s rRNA phylogenies differ from laboratory to laboratory. In 1999, evolutionary biologist Michael Lynch wrote: “Clarification of the phylogenetic relationships of the major animal phyla has been an elusive problem, with analyses based on different genes and even different analyses based on the same gene yielding a diversity of phylogenetic trees.”

    Lynch was optimistic that with improved methods molecular phylogeny would clarify relationships among the animal phyla. Despite the continuing efforts of many researchers, however, conflicts among molecular phylogenies of the major animal groups have not just persisted, but grown.

    – Jonathan Wells, The Politically Incorrect Guide to Darwinism and Intelligent Design

    From what I’ve read on the subject, the parameters you use for tuning your trees can also result in different trees.

    Theobald is really big on pushing the line that the trees really aren’t that different, but everyone else I’ve read regarding the topic acknowledges that the problems are real. I don’t know enough on the topic to be dogmatic either way, but I’ve read enough to make me highly skeptical of Theobald’s pronouncements.

    Atom

  9. Atom,

    Theobald is aware that these methods, like everything else in science, are imperfect. He devotes an entire section to a discussion of what it means when phylogenetic trees disagree:

    Some Statistics of Incongruent Phylogenetic Trees

    But the question is not whether phylogenetic trees always match perfectly. If they did, it would be miraculous! The real question is how well they match, and with what degree of statistical significance.

    Theobald gives the example of two mismatching crocodile phylogenies, one generated from morphological data and another from the nucleotide sequence of a proto-oncogene. Even though the trees differ, the probability that they would match as well as they do, purely by chance, is less than 0.08%!

    If that weren’t impressive enough, the researchers generated another tree, this time based on mitochondrial genes. The new tree was exactly the same as the tree based on the proto-oncogene.

    The probability of getting this kind of match between three independent trees, purely by chance, is less than 8 millionths of one percent.

    As Theobald points out, even many biologists are unaware of the staggering numbers involved:

    The stunning degree of match between even the most incongruent phylogenetic trees found in the biological literature is widely unappreciated, mainly because most people (including many biologists) are unaware of the mathematics involved (Bryant et al. 2002; Penny et al. 1982; Penny and Hendy 1986). Penny and Hendy have performed a series of detailed statistical analyses of the significance of incongruent phylogenetic trees, and here is their conclusion:

    “Biologists seem to seek the ‘The One Tree’ and appear not to be satisfied by a range of options. However, there is no logical difficulty in having a range of trees. There are 34,459,425 possible [unrooted] trees for 11 taxa (Penny et al. 1982), and to reduce this to the order of 10-50 trees is analogous to an accuracy of measurement of approximately one part in 10^6.” (Penny and Hendy 1986, p. 414)

  10. 10
    Cornelius Hunter

    Hoki (3):

    Why not? They are, presumably, environments with light?

    Yes, you are correct. Both environments did have light. But that is about where the similarity ends and differences begin. Big differences. Indeed, if all that was required to evolve strikingly similar vision systems was the mere presence of light, then we’d see similar systems throughout biology. But of course we don’t. When evolutionists give this sort of response it shows they are grasping.

    mereologist (4):

    In the future, you would do well to understand how such research is done before presuming to criticize it as “not motivated by the evidence”.

    I do understand how it was done.

    The 38 decimal places come from the fact that the 30 taxa can be arranged into more than 10^38 possible trees, yet independent morphological and molecular studies converge on the same tree. This is stupendous evidence for common descent.

    That is false.

    The odds of it happening by chance are less than 1 in 10^38; thus we say that the standard phylogenetic tree is known to an accuracy of better than 38 decimal places.

    Thus revealing your metaphysics. Folks, it never was about science, and nothing has changed in that regard. Here’s just a short explanation.

    You and others who dismiss common descent should ponder this long and hard.

    I have.

    It implies that either common descent is true, or the designer has made it appear, overwhelmingly, to be true.

    Again, that is false.

    Either way, you you have to ignore the evidence — all 38 decimal places worth — to conclude that common descent is false.

    When I first heard what they say about statistics, I thought it was a joke.

    I should add that ID supporters who accept common descent are not off the hook either. If the designer uses common descent but either front-loads information or intervenes and adds it during the development of life, then there is no reason for the molecular data to conform to the same standard tree as the morphological data. The designer could have chosen one of the trillions of trillions of schemes that would have caused a mismatch between the two.

    Another good example of non evolutionary views being evaluated according to evolutionary assumptions.

    Either undirected evolution is true, or the designer has made it appear, overwhelmingly, to be true. Either way, you you have to ignore the evidence — all 38 decimal places’ worth — to conclude that ID is correct. It’s surprising to me that so few ID supporters recognize the magnitude of the problem. When ID critics talk about “overwhelming evidence”, they aren’t kidding!

    I agree they aren’t kidding. The religion in evolution is used to form a valid argument, and evolutionists absolutely believe in it.

    But don’t be surprised about IDers. They are much more on the empirical side of things. They don’t bring the kinds of powerful religious commitments that evolutionists do.

    mereologist, you’re giving a classic example of the religion in evolution, and its subtlety. You’re obviously a pretty smart fellow, and I suspect you’re convinced that you are quite free of any religious or metaphysical premises.

  11. Mereologist,
    “If the designer uses common descent but either front-loads information or intervenes and adds it during the development of life, then there is no reason for the molecular data to conform to the same standard tree as the morphological data. The designer could have chosen one of the trillions of trillions of schemes that would have caused a mismatch between the two.”

    When you mention two systems here, the molecular and morphological, are you actually talking about the genome and the body? Please explain, you say ID’d common descent isn’t off the hook, I don’t understand at all.

    Also, are you off the hook with the neodarwin ToL or are there major major unresolved issues?

  12. 12

    If this guy is trying to say body plans are related to the genetic code he is either on drugs or needs to start taking them:

    For prime example of the flimsy “similarity evidence” used by materialists to try to make their case for evolution, most materialists are adamant that 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.

    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
    http://www.evolutionnews.org/2.....footnote19

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

    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 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. On top of that 80% difference in proteins, the oft quoted 98.8% DNA similarity is not even 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 that 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

    Eighty percent of proteins are different between humans and chimpanzees; Gene; Volume 346, 14 February 2005:
    The early genome comparison by DNA hybridization techniques suggested a nucleotide difference of 1–2%. Recently, direct nucleotide sequencing confirmed this estimate. These findings generated the common belief that the human is extremely close to the chimpanzee at the genetic level. However, if one looks at proteins, which are mainly responsible for phenotypic differences, the picture is quite different, and about 80% of proteins are different between the two species.

    He seem to be hung up on the 38 decimal places thing,,,well we got a few decimal places for evolution to explain, how about one hundred and ten thousand decimal places for starters:

    In Barrow and Tippler’s book The Anthropic Cosmological Principle, they list ten steps necessary in the course of human evolution, each of which, is so improbable that if left to happen by chance alone, the sun would have ceased to be a main sequence star and would have incinerated the earth. They estimate that the odds of the evolution (by chance) of the human genome is somewhere between 4 to the negative 180th power, to the 110,000th power, and 4 to the negative 360th power, to the 110,000th power. Therefore, if evolution did occur, it literally would have been a miracle and evidence for the existence of God. William Lane Craig

    William Lane Craig – If Human Evolution Did Occur It Was A Miracle – video
    http://www.youtube.com/watch?v=GUxm8dXLRpA

  13. Cornelius,

    But don’t be surprised about IDers. They are much more on the empirical side of things. They don’t bring the kinds of powerful religious commitments that evolutionists do.

    But do IDers sometimes buy into these evolutionist religious assumptions as well? Michael Behe argues for common descent in The Edge of Evolution using some examples of “pseudogenes”. He even claims, after a discussion of hemoglobin genes, “It’s hard to imagine how there could be stronger evidence for common ancestry of chimps and humans”.

    What

    What

  14. Heh—accidentally hit return. :D

    Anyway I was just going to ask what the appropriate stance for IDers is in the face of this data.

  15. 15

    lamark, you said:

    When you mention two systems here, the molecular and morphological, are you actually talking about the genome and the body?

    Arrange a family tree of the animal kingdom using JUST skeletal and body form data. Regardless of your assumptions, humans and chimps will inevitably be grouped together, sharks with rays, big cats with small cats, etc.

    Now, do the same with JUST genetic data, such as the cytochrome c studies.

    The point is that the SAME tree emerges from BOTH independent data sets.

    bornagain77, you said:

    Darwinian evolution is proven true when we look at the supposed 98.8% genetic similarity between chimps and man.

    OK then, if that’s not good enough for you, then how about:

    - Humans and chimps have seven transposons of the Alu family in the SAME location on the genome in the SAME order. link Transposons cannot leave the genome and can ONLY be passed through inheritance.

    - Humans and chimps share several endogenous retroviruses, in the SAME order, on the SAME spot on the genome. link. ERVs can only be passed via inheritance.

    - Humans and chimps both have two copies of the 21-hydroxylase gene, one functional and one non-functional. The non-functional one is rendered so via the SAME mutation in BOTH genomes: link

    - Humans and all primates are incapable of manufacturing their own vitamin C, due to a faulty gene. The mutation that renders it faulty is the SAME mutation in the entire primate family: link In contrast, guinea pigs are also unable to manufacture vitamin C, but a DIFFERENT mutation inactivates in their family tree.

  16. Cornelius writes:

    That is false… Again, that is false… When I first heard what they say about statistics, I thought it was a joke…

    Cornelius,

    It is customary when debating to explain why your opponent’s argument fails versus simply asserting that it does. The latter won’t persuade anyone.

    mereologist, you’re giving a classic example of the religion in evolution, and its subtlety. You’re obviously a pretty smart fellow, and I suspect you’re convinced that you are quite free of any religious or metaphysical premises.

    Several of us explained to you in an earlier thread why it is essential to make assumptions about the designer. If you don’t — and this is as true for the ID supporter as it is for the critic — then the designer hypothesis is not falsifiable, and therefore cannot be examined scientifically.

    Setting that aside, of course I make metaphysical assumptions. For example, I assume that objective reality exists and that we can learn about it through science. Do you find that assumption objectionable?

    Finally, since you say that I am “giving a classic example of the religion in evolution”, let’s get specific. Tell me what religion assumptions you think I am making, why they are invalid, and what assumptions you would replace them with in order to produce a falsifiable designer hypothesis.

  17. SingBlueSilver,
    Gene and phenotype homology match between different species? No they don’t, below is a video covering this. I’m not totally clear on what you’re saying I need something more specific.

    /watch?v=pMVBFJCqFXc&feature=email

    But my question was, why is ID not off the hook in regards to an ID’d tree of life? Mereologist too is being vague.

  18. Cornelius Hunter:

    Yes, you are correct. Both environments did have light. But that is about where the similarity ends and differences begin. Big differences. Indeed, if all that was required to evolve strikingly similar vision systems was the mere presence of light, then we’d see similar systems throughout biology. But of course we don’t. When evolutionists give this sort of response it shows they are grasping.

    Both have camera eyes. But that is about where the similarity ends and differences begin. Are you grasping?

    P.S. I have left a comment in your recent Sober thread I was really hoping you could respond to. If you have the time.

  19. lamarck asks:

    Please explain, you say ID’d common descent isn’t off the hook, I don’t understand at all.

    Here’s why. Suppose that common descent is true, but that there is a designer who front-loads genetic information into the common ancestor of all organisms.

    If the information is front-loaded, all kinds of crazy things are possible (this is also true if the designer actively intervenes during evolution). For example, there is no reason (other than the designer’s whims) why complicated features involving thousands of genes can’t arise in a single generation. There’s no reason why exactly the same complicated feature — down to the same genes, with the same mutations — can’t arise independently in two completely unrelated species. There’s no reason why a feature can’t appear in an ancestor, then disappear in all of it’s descendants, only to appear again sometime later in exactly the same form. There’s even no reason why an amoeba cannot “give birth” to a human zygote. It all depends on what the designer decides.

    All of these possibilities mean that guided common descent can violate the assumptions on which phylogenetic reconstructions rest. The designer could make things so that it was impossible to reconstruct a phylogenetic tree. To use Theobald’s example, the designer could make the cytochrome c tree look completely different from the morphological tree. If there is a designer, then the only way that life can appear the way it does is if the designer chose to guide evolution in a way that mimics unguided evolution.

    The upshot is that even if you, as an ID supporter, accept common descent, the facts force you to assume that the designer guided evolution in a way that makes it appear to be unguided. In other words, the only way you can accept intelligent design is to ignore the evidence and take ID on faith. It is thus a religious position, not a scientific one.

    Also, are you off the hook with the neodarwin ToL or are there major major unresolved issues?

    The only issue I’m aware of with regard to the tree of life is that the word “tree” is a slight oversimplification. Near the root, the “tree” is more like a “net” due to horizontal gene transfer between organisms. Otherwise there are no issues. There is no dispute over the fact that the mammals, for example, form a tree, and that we share a common ancestor with chimpanzees.

  20. Cornelius Hunter:

    mereologist:
    The designer could have chosen one of the trillions of trillions of schemes that would have caused a mismatch between the two.

    Another good example of non evolutionary views being evaluated according to evolutionary assumptions.

    Bayesian, rather than evolutionary, I would say. You have to make religious assumptions (your term, I believe?) in order to claim anything about what the designer would do. You know, the same sort of assumptions you accused Sober of doing (when he didn’t).

  21. Mereologist, But looking at the genome we only see one thing. That it appears to go from a seemingly designed point to a chaotic point.

    AND YOU CAN’T GET NEW CSI on the order of genes coding for whole different systems into the genome, you can only modify existing stuff slightly but no larger morphology. This isn’t just some aspect that holds darwinist back, it’s everything. It all depends on this and we only see the opposite of theory.

    Your comment that ID can’t be science because things appear unguided should read “things only look guided. Even the environment itself hardly has an effect on change from what’s observed.”

    Where do you see unguided evidence? I don’t see any. Is it only because you can’t conceive of an elastic genome program that allows for new conditions but retains brackets?

  22. Mereologist, why don’t you just come out and say the cambrian explosion is solved by lateral gene transfer? That way I can correct you.

  23. 23

    Sing blue silver:

    refutation of cytochrome c is here:

    If the existence of cytochrome C in “higher forms” of animals is the result of evolution from a common ancestor, then one would expect to see a logical progression. That is, the cytochrome C of an invertebrate (like a worm) would be slightly different from a bacteria. A “primitive” vertebrate (like a fish) would have those same differences, plus a few more. As you progress along the presumed evolutionary path to amphibians, reptiles, mammals, primates, ending with humans, you should see the changes in cytochrome C accumulate.

    On the other hand, if cytochrome C is a commonly used component employed by a designer, you will not see that logical progression. You will just see minor differences which optimize cytochrome C for that kind of creature.

    However, the most striking feature of the matrix is that every identifiable subclass is isolated and distinct. Every sequence can be unambiguously assigned to a particular subclass. No sequence or group of sequences can be designated as intermediate with respect to other groups. All the sequences of each subclass are equally isolated from the members of another group. Transitional or intermediate classes are completely absent from the matrix. 4

    http://www.ridgecrest.ca.us/~d.....v7i10f.htm

    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:

    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.
    http://www.ncbi.nlm.nih.gov/pubmed/12547679

    The problem is that the 98.8% similarity is not “good enough” from a scientific perspective. As i clearly showed the 98.8 percent similarity is illusory, and derived from biased methodology.

    The question you should be truly asking yourself is why cling to such evidence when it has no solid foundation in science that can withstand scrutiny?

    It clearly is not the practice of good science for you to do as such!

  24. 24

    lamarck,

    Gene and phenotype homology match between different species? No they don’t…

    Yes, they do. This is not in dispute:

    Estimating the reliability of evolutionary trees

    Estimating the reliability of evolutionary trees

    The degree of correlation between different trees is more precise than our measurements of GRAVITY. We know LESS about gravity than we do about the relationships of organisms to one another.

    Your video doesn’t work.

    bornagain77,

    Cytochrome C and 98% chimp/human DNA match.

    Read again what I posted. Chimps and humans share RANDOMLY INSERTED ERVs and transposons in the SAME SPOT on the genome in the SAME order. These genetic elements can ONLY be acquired through inheritance. This is the same type of evidence used to prove fatherhood on Jerry Springer.

    This is the closest we will ever get to absolute proof of common ancestry.

  25. 25

    SingBlueSilver,
    You are assuming non-functionality of the genome (shared errors of ERV’s) to make your argument, yet high level regulatory function is found for ERV’s thus precluding the very foundation of your argument in the first place.

    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

    Endogenous Retroviruses and LTR retrotransposons
    Talk Origins has this to say of Endogenous Retroviruses:
    Endogenous retroviruses are molecular remnants of a past parasitic viral infection. Occasionally, copies of
    a retrovirus genome are found in its host’s genome, and these retroviral gene copies are called endogenous
    retroviral sequences.
    7
    Essentially all of these endogenous retroviruses contain mutations that would disrupt the function of their
    genes, as would be expected if they inserted millions of years ago with no selective pressure to maintain the function of the genes.
    Here’s what some recent scientific evidence says about Endogenous Retroviruses:
    They show up expressed in many cell tissues http://jvi.asm.org/cgi/content/full/79/1/341
    Human tissues that lack HERV transcription could not be found, confirming that human endogenous
    retroviruses are permanent components of the human transcriptome. Distinct activity patterns may reflect
    the characteristics of the regulatory machinery in these cells, e.g., cell type-dependent occurrence of transcriptional regulatory factors.
    ERVWE1 provirus necessary for placental development in humans, chimpanzee, gorilla, orangutan,
    and gibbon (common function – not shared error) http://www.pnas.org/cgi/content/full/101/6/1731
    We show in this article that the ERVWE1 locus is functionally preserved in the human population and in the identified orthologous locus of chimpanzee, gorilla, orangutan, and gibbon.

    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.
    http://www.ncbi.nlm.nih.gov/pubmed/12547679

    Here is the last statement of the ENCODE study which gave strong indication of 100% functionality of the genome and undermined the “junk DNA you so desperately need to make your argument for “shared errors”.

    Concluding statement of the ENCODE study:
    “we have also encountered a remarkable excess of experimentally identified functional elements lacking evolutionary constraint, and these cannot be dismissed for technical reasons. This is perhaps the biggest surprise of the pilot phase of the ENCODE Project, and suggests that we take a more ‘neutral’ view of many of the functions conferred by the genome.”
    http://www.genome.gov/Pages/Re.....e05874.pdf

    “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. A central cluster of chromocenters surrounded by a layer of LINE-dense heterochromatin enables the nucleus to be a converging lens for photons, so that the latter can pass without hindrance to the rod outer segments that sense light. In other words, the genome regions with the highest refractive index — undoubtedly enhanced by the proteins bound to the repetitive DNA — are concentrated in the interior, followed by the sequences with the next highest level of refractivity, to prevent against the scattering of light. 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. -
    http://www.evolutionnews.org/2......html#more

  26. 26

    bornagain77

    Nowhere did I say anything about whether ERVs provided function or not. That is not the argument.

    ERVs are retroviruses that have RANDOMLY invaded the germ line cells, and become part of the genome. They are then passed on to descendants.

    We humans share several of the EXACT SAME ERVs in the SAME place in the SAME order on the genome.

  27. bornagain77,

    That is, the cytochrome C of an invertebrate (like a worm) would be slightly different from a bacteria. A “primitive” vertebrate (like a fish) would have those same differences, plus a few more. As you progress along the presumed evolutionary path to amphibians, reptiles, mammals, primates, ending with humans, you should see the changes in cytochrome C accumulate.

    Thanks for posting the links. Your cytochrome C argument sounds very similar to one used by Denton in his book Evolution: A Theory in Crisis, however, and IIRC, he doesn’t use that argument anymore. At the moment, I can only find a few snarky evolutionist links discussing the issue, but if you look around you might have more luck.

    I’m more interested in the philosophical issues raised by Cornelius’ post, however. When you say:

    On the other hand, if cytochrome C is a commonly used component employed by a designer, you will not see that logical progression. You will just see minor differences which optimize cytochrome C for that kind of creature.

    isn’t that a judgment about the Designer, and hence (at least for Christian IDers) a religious statement?

    Let me finally pose a hypothetical question: Suppose the cytochrome C, hemoglobin, and ERV data was all perfectly consistent with common ancestry, to the best of your knowledge. Would you draw any conclusions from that evidence? I’m asking because I think Cornelius takes quite a different tack here—even in the face of extraordinary correlations and patterns, I take it he would say you could not conclude common ancestry without invoking religious premises.

  28. 28

    SingBluesilver,
    As I have learned through the years debating materialists, It is pointless to discuss an issue with someone who refuses to acknowledge the flaws of there assumptions. Thus I will politely refrain from correcting your errors of argument.

    Herb,
    Even if all the data linked up for common ancestry, which is not the case since we are finding more and more that great differences are to be found, I would still find that evolutionists have ignored the foundational principle of science (The Second Law) in order to make their case for unguided (non-teleological) common ancestry. i.e. even if similarity could be established, materialists still have not made their case for non-teleological evolution due to the established overwhelmingly negative mutation rates which reflect exactly what we would expect operating from first principles of science.

  29. 29

    SingBlueSilver,

    ——”Read again what I posted. Chimps and humans share RANDOMLY INSERTED ERVs and transposons in the SAME SPOT on the genome in the SAME order. These genetic elements can ONLY be acquired through inheritance.”

    That’s actually not true.
    http://www.detectingdesign.com.....Endogenous

  30. BA77,

    Thanks for responding to my questions. Just one further clarification: I take it in the first sentence you are referring to the second law of thermodynamics?

  31. 31

    Herb,
    Yes , the second law. But a more precise principle is found for biology which combines the second law with the law of conservation of information and it is called Genetic Entropy. Though the principle is, IMO, only roughly outlined right now it holds for all adaptions in biology that I can find as well as explaining many discrepancies of biology that are just glossed over in evolutionary thought. i.e.evolutionists never seem to get past the “we are surprised by this result” phase of research.

  32. bornagain77,

    But a more precise principle is found for biology which combines the second law with the law of conservation of information and it is called Genetic Entropy.

    Thanks. I’d heard the term “Genetic Entropy” before but hadn’t looked into it in detail. It certainly has some interesting implications concerning the age of the human race, and our survival!

  33. bornagain77:

    Exactly how does the fact that the amount of energy available for work will always show an average decrease relate to ‘information’?

  34. 34

    Clive,

    That’s actually not true.
    http://www.detectingdesign.com…..Endogenous

    That article goes on and on about functionality, which I am not disputing. Genes picked up from ERVs can be recruited for other purposes.

    It then goes on to say that there are inconsistencies in ape/human phylogenies. I do not dispute this either. There are lots of disagreements about the specific details among biologists.

    Then it goes into the possibility that, since our genome contains 30,000 ERVs, it is possible that 7 of them are there by chance.

    In a genome of 3 billion base pairs. In the same order.

    It isn’t JUST the ERVs that prove common descent. What about the Alu transposon? Same thing. How about the vitamin C mutation that is the same in all primates including humans, but not in guinea pigs? Same thing.

    The article then says that maybe apes and humans, being prone to retroviral infections, got infected at the same time.

    In the same place on the genome? In the same order?!

    What about transposons? These are viruses that lack a coat protein and cannot leave the genome. We share several with chimps.

    And all the above ONLY on animals that have a predicted common ancestor, but not on ones that do not.

  35. 35

    bornagain77:

    As I have learned through the years debating materialists, It is pointless to discuss an issue with someone who refuses to acknowledge the flaws of there assumptions. Thus I will politely refrain from correcting your errors of argument.

    I showed you DNA fingerprints indicative of common descent. You responded that the fingerprints are not non-functional. I responded that I never said that, and I reiterated my original argument.

    You then poison the well by saying “materialists” refuse to acknowledge the flaws of their assumptions.

    I.E., you never responded to my original argument at all, and now you attack me personally.

    ???

  36. 36

    Still awaiting Cornelius Hunter’s reply to the challenge I posed in an earlier comment.

    Meanwhile, here’s yet more evidence for common descent:

    Dinosaur Fossils Fit Perfectly Into The Evolutionary Tree Of Life, Study Finds

    ScienceDaily (Jan. 30, 2009) — A recent study by researchers at the University of Bath and London’s Natural History Museum has found that scientists’ knowledge of the evolution of dinosaurs is remarkably complete.

    Evolutionary biologists use two ways to study the evolution of prehistoric plants and animals: firstly they use radioactive dating techniques to put fossils in chronological order according to the age of the rocks in which they are found (stratigraphy); secondly they observe and classify the characteristics of fossilised remains according to their relatedness (morphology).

    Dr Matthew Wills from the University of Bath’s Department of Biology & Biochemistry worked with Dr Paul Barrett from the Natural History Museum and Julia Heathcote at Birkbeck College (London) to analyse statistical data from fossils of the four major groups of dinosaur to see how closely they matched their trees of evolutionary relatedness.

    The researchers found that the fossil record for the dinosaurs studied, ranging from gigantic sauropods to two-legged meat eaters such as T. rex, matched very well with the evolutionary tree, meaning that the current view of evolution of these creatures is very accurate.

  37. SingBluesilver,
    What do you mean yes they do? No, they do not.

    To watch the video type in:

    Investigating Evolution: Homology

    in youtube.

  38. 38

    I posted this link on another thread, might be useful here to get some up to speed on the basics if needed.

    http://www.teachertube.com/vie.....n_Ancestry

    I’m interested to hear what the flaw in the argument is. Clive’s link does seem to be rebutted by the simple probability issue SingBlueSilver details in a previous comment. Admittedly Clive has not yet responded with specifics so I’ll await his thoughts on why that is (presumably) not the case.

  39. 39

    We should note that the link Clive provides

    http://www.detectingdesign.com.....Endogenous

    Is to a creationist website.

    Sean D. Pitman M.D. is a creationist. He believes in a literal Noah’s Ark

    http://www.detectingdesign.com/DesmondFord.html

    He has a bio on creation Wiki

    http://creationwiki.org/Sean_D._Pitman

    His work on his website is not peer reviewed. It’s just a website.

    And this is how you rebut

    Chimps and humans share RANDOMLY INSERTED ERVs and transposons in the SAME SPOT on the genome in the SAME order. These genetic elements can ONLY be acquired through inheritance.

    by linking to a person who probably believes the earth is 10,000 or less years old?

    Unlike some here I click on the links provided as ironclad rebuttals.

    That’s actually not true.

    You’ll have to do better then that, provide a specific argument addressing a specific point or concede. Argument et linkum won’t cut it if the link is to a creationist.

    You are not a YEC are you Clive? If not, why link to one as evidence in a argument?

  40. 40

    I said

    Argument et linkum won’t cut it if the link is to a creationist.

    To preempt:
    That’s of course not to say that it’s impossible a creationist could have something worthwhile to say. But the moment you introduce creationism or a “literal Noah’s Ark” the science hat comes right off.

    And that link?

    You want people to wade through that?

    You get it fact checked and peer reviewed first.

    There is only so much time in the day!

  41. 41

    Echidna,

    A man can make an argument regardless of whether he is YEC or not as a belief within the whole spectrum that makes up his worldview. I don’t rule everything you write out because you disbelieve in your own soul and are an atheistic materialist. If a persons other beliefs made a person incredible as a whole on any subject whatsoever, I would never consider anything you have to say on anything, including a recipe for cooking pasta, so the same respect should be extended by you.

    And you know, it’s this sort of thing that troubles me about you. You compare YEC to hobos, everything they may ever say is ruled out of hand by your bias, that I begin to find you unreasonable in general.

  42. 42
    Cornelius Hunter

    mereologist (16):

    I responded in a new post.

  43. 43

    Clive

    A man can make an argument regardless of whether he is YEC or not as a belief within the whole spectrum that makes up his worldview.

    Yes indeed. I said as much in my own follow up comment.

    The question is, is the argument scientific? Given that it’s clear that the website espouses a creationist viewpoint why should they get special treatment?

    What I’m saying is that you are attempting to rebut a scientific point with somebody’s simple opinion.

    If it’s indeed the case that the website has disproved one of the foundational pieces of the puzzle, namely the understanding of how ERVs and transposons contribute to our understanding of common descent, then I would suggest he writes it up and sends it to Nature.

    If he sticks to the science it’ll have the same chance of publication as any other paper.

    So yes, a man can make an argument regardless of if he is a YEC or not, but if he is a self proclaimed YEC who believes in a literal Noah’s Ark then that sends a signal right there.

    So, do you have a specific data point from the link you gave to the YEC site that rebuts the contention that

    Chimps and humans share RANDOMLY INSERTED ERVs and transposons in the SAME SPOT on the genome in the SAME order. These genetic elements can ONLY be acquired through inheritance.

    or not? What specific part in that rather large, rambling website rebuts that exact point? Can you make the argument yourself?

    I can link to many more things, most of which will be peer reviewed that make the opposite case that the link you gave is making. Do I then win? Argument by number of links?

    I don’t rule everything you write out because you disbelieve in your own soul and are an atheistic materialist.

    And I don’t rule out everthing that you say because you believe in ghosts, you don’t support your points and think sarcasm counts as an argument.

    If a persons other beliefs made a person incredible as a whole on any subject whatsoever, I would never consider anything you have to say on anything, including a recipe for cooking pasta, so the same respect should be extended by you.

    And I’m doing that by asking you to engage on the issue at hand rather then simply provide a link and saying “there, that proves it”.

    I can create a website that says “Common descent is true”. If I provide a link to that website, will I have proven my case? That’s essentially what you have just done.

    You compare YEC to hobos, everything they may ever say is ruled out of hand by your bias, that I begin to find you unreasonable in general.

    That’s simply not true as anyone who’s read the thread in question can attest to. I said asking a creationist for an opinion on the age of the earth is like asking a hobo for financial advice. They’ve already made their unsuitability for the role obvious. The hobo by having no money, the creationist by having a scientifically unsupportable and discredited view on the age of the earth.

    And yes, you can ban me if you prefer. It won’t make any difference to the strength or support for your argument (or link).

    The more this goes on, the more it believe you are a YEC Clive.

    Will you say that you are not a YEC Clive or not?

  44. 44

    Cornelious

    Contradictory data are usually filtered out long before the analysis step, thus improving the fit. Evolutionists make all kinds of erroneous claims about how astronomically well the data fit their theory.

    Can you give a specific example or two of that happening?

    If not, well, it seems to undermine your entire argument as to the accuracy of “evolution”.

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