Monday, April 11, 2011

Karl Giberson: Broken Genes Prove Evolution

In yesterday’s CNN blog evolutionist Karl Giberson bemoans the influence of religious thinking in beliefs about origins and then, in evolutionary typical fashion, hypocritically mandates evolution’s own religious beliefs.

when it comes to the truth of evolution, many Christians feel compelled to look the other way … While Genesis contains wonderful insights into the relationship between God and the creation, it simply does not contain scientific ideas about the origin of the universe, the age of the earth or the development of life.

So religious beliefs should not inform our views on origins, got it.

And all life forms are related to each other though evolution. These are important truths that science has discovered through careful research.

Scientific research has revealed on such thing. Not even close.


Anyone who values truth must take these ideas seriously, for they have been established as true beyond any reasonable doubt.

This is the universal claim of evolutionists, but it has never been even remotely demonstrated scientifically.


There is much evidence for evolution.

There is much evidence for geocentrism.


The most compelling comes from the study of genes, especially now that the Human Genome Project has been completed and the genomes of many other species being constantly mapped.

In particular, humans share an unfortunate “broken gene” with many other primates, including chimpanzees, orangutans, and macaques. This gene, which works fine in most mammals, enables the production of Vitamin C. Species with broken versions of the gene can’t make Vitamin C and must get it from foods like oranges and lemons.

These similar broken genes (the so-called pseudogenes) are found with broken parts that do not fit the expected evolutionary pattern. In these cases even evolutionists admit that the breaks are not due to common descent. It is therefore the fallacy of special pleading to claim that when such breaks fit the expected evolutionary pattern they serve as proof texts for evolution.

Of course none of this matters because the argument was never scientific to begin with.

Thousands of hapless sailors died painful deaths scurvy during the age of exploration because their “Vitamin C” gene was broken.

How can different species have identical broken genes? The only reasonable explanation is that they inherited it from a common ancestor.

The only reasonable explanation is common descent? It is the umpteenth time evolutionists have proclaimed their metaphysics in the guise of science. And it is the umpteenth time they have done this right after insisting religion must have nothing to do with origins science. You can read more about this here, here, here, here and here. Simply put, this claim that the only reasonable explanation for pseudogenes is common descent does not come from science—it can’t.

Such evidence proves common ancestry with a level of certainty comparable to the evidence that the earth goes around the sun.

True, given the evolutionist’s religious mandates, evolution is highly certain. But from a scientific perspective the idea has substantial problems.

This is but one of many, many evidences that support the truth of evolution

True, evolution’s religious view converts a great many unlikely evidences into proof texts. Religion drives science, and it matters.

685 comments:

  1. Not sure if it's worth repeating that "Is not" doesn't constitute much of an argument.

    And all life forms are related to each other though evolution.

    Yes, that has been well-established by science.

    ReplyDelete
  2. These similar broken genes (the so-called pseudogenes) are found in patterns that do not fit the expected evolutionary pattern.

    Any references to the primary literature on that point?

    In these cases even evolutionists admit that they are not due to common descent.

    Primary literature references?

    ReplyDelete
  3. Pedant said...

    These similar broken genes (the so-called pseudogenes) are found in patterns that do not fit the expected evolutionary pattern.

    Any references to the primary literature on that point?

    In these cases even evolutionists admit that they are not due to common descent.

    Primary literature references?


    Cornelius doesn't 'do' the primary scientific literature. It's too much trouble. Since this blog is written as propaganda for his scientifically illiterate IDC sycophants, there's no need for him to be technically accurate, or back up his bombastic rhetoric.

    "Making it up as you go" has always been a key component of every Creationist argument. Cornelius has embraced the style with open arms.

    ReplyDelete
  4. Zachriel said, "And all life forms are related to each other though evolution.

    Yes, that has been well-established by science"

    ---

    It's those kind of exaggerated statements inform me of just how ridiculous and sloppy this whole sordid field of evolutionary study is.

    Matter of fact words like, "ALL", "WELL-ESTABLISHED" is nothing but over the top hogwash. This is not careful and methodical science, it is akin to reading tea leaves.

    ReplyDelete
  5. Cornelius: "These similar broken genes (the so-called pseudogenes) are found in patterns that do not fit the expected evolutionary pattern."

    Cornelius, I think we're approaching the one year anniversary of the first time I asked you this question: Can you give examples of pseudogenes that don't fit the expected evolutionary pattern? (my guess is 'no')

    Cornelius: "The only reasonable explanation is common descent? It is the umpteenth time evolutionists have proclaimed their metaphysics in the guise of science."

    Say we found a series of two dozen animal tracks by a riverbed in Africa. they are consistent in size, shape, and stride with elephant tracks, and inconsistent in size, shape, and stride with any other known animal. Am I then off my rocker if I say: "The only reasonable explanation is that an elephant made these tracks?" Am I introducing metaphysics into the conversation because I haven't considered an unspecified, undocumented, unverified animal made the tracks as a likely possibility?

    ReplyDelete
  6. Neal, three questions for you, one at a time:

    1. Do you think paternity tests are reliable? If someone wrongly accused you of fathering an illegitimate child, and a paternity test confirmed that you were not the father, would you consider yourself vindicated by the test?

    ReplyDelete
  7. Derick, try running paternity tests on all species and see if they all come back as positive! Your analogy is flawed. Seriously?

    Out of time for now. More to follow for you and Scott

    ReplyDelete
  8. CH: "These similar broken genes (the so-called pseudogenes) are found in patterns that do not fit the expected evolutionary pattern. In these cases even evolutionists admit that they are not due to common descent."

    Whaa? Can I buy a link?

    ReplyDelete
  9. Derick:

    ===

    Say we found a series of two dozen animal tracks by a riverbed in Africa. they are consistent in size, shape, and stride with elephant tracks, and inconsistent in size, shape, and stride with any other known animal. Am I then off my rocker if I say: "The only reasonable explanation is that an elephant made these tracks?" Am I introducing metaphysics into the conversation because I haven't considered an unspecified, undocumented, unverified animal made the tracks as a likely possibility?
    ===

    If you're going to make this argument, then (i) briefly mention the alternatives and why they were ruled out and (ii) briefly mention the status of the explanation you are proposing.

    Evolutionists do the former but not the latter. In the former, they explain that no designer would have created pseudogenes. In the latter, they sometimes fail to explain that evolution has substantial scientific problems, they in fact misrepresent the science, saying there are no substantial scientific problems.

    ReplyDelete
  10. Tedford the idiot said...

    Derick, try running paternity tests on all species and see if they all come back as positive! Your analogy is flawed. Seriously?


    Seriously Tedford, you are a clueless idiot.

    DNA comparisons are used all the time for establishing ancestral relationships.

    They can be used to establish direct paternity as described above.

    They can be used to establish more distant relationships, as the descendants of slave Sally Hemings were linked to Thomas Jefferson.

    They can be used to establish the relationships between large groups of even more distantly related people, as Canadian and Alaskan Inuits have been genetically identified as closely related to indigenous Siberian and Mongolian populations.

    The exact same techniques are also used to establish the relationships between species, such as humans and chimps sharing a common ancestor approx. 6 MYA.

    Why don't you tell us why the techniques work and are accepted in the first three cases, but suddenly become invalid in the fourth case.

    ReplyDelete
  11. "They sometimes fail to explain that evolution has substantial scientific problems"

    Maybe you should define the 'substantial scientific problems'. Controversies,yes. Works in progress, yes. But substantial problems? I've yet to see one here, that you've actually interpreted the evidence for correctly, that presents a falsification of common descent.

    ReplyDelete
  12. Cornelius Hunter said...

    Evolutionists do the former but not the latter. In the former, they explain that no designer would have created pseudogenes. In the latter, they sometimes fail to explain that evolution has substantial scientific problems, they in fact misrepresent the science, saying there are no substantial scientific problems.


    Sorry Cornelius, but only in your little fantasy Creationist world does your bellyaching "ToE can't explain everything to my personal satisfaction!!" count as substantial scientific problems.

    Guess you'll just have to live with the disappointment.

    ReplyDelete
  13. Neal: Derick, try running paternity tests on all species and see if they all come back as positive! Your analogy is flawed. Seriously?

    Neal, you seem to have a pathological aversion to answering simple, direct yes or no questions. My question had nothing to do with other species. I'm taking about human paternity tests. And apparently, you can't distinguish between an analogy and a question. I made no analogy in my question to you.

    I'll rephrase for simplicity and clarity:

    1. Do you think that paternity tests are a reliable means of determining human paternity? Yes, or no.

    (typing either a two or three word response shouldn't demand much of your time)

    ReplyDelete
  14. Cornelius: "If you're going to make this argument, then (i) briefly mention the alternatives and why they were ruled out and (ii) briefly mention the status of the explanation you are proposing."

    I believe I did already.

    (i) the footprints are not consistent in size, shape, or stride with any other known animal; rhinos, hippos, lions, hyenas, pandas, kangaroos, polar bears, turtles, antelopes, geese, etc. We of course cannot rule out chupacabras, yetis, dragons, pixies, or centaurs, but that is of no consequence.

    (ii) With a reasonable degree of certainty, one can say that upon finding elephant tracks, it is a fact that elephants were in the area at one point in the past. With more corroborating evidence, such as elephant stool or elephant blood (from an attack) the fact of the elephant's presence can be asserted with a higher and higher degree of certainty.

    ReplyDelete
  15. How can different species have identical broken genes? The only reasonable explanation is that they inherited it from a common ancestor.

    The only reasonable explanation is common descent?


    It would be nice if you could sketch some alternative explanations so we can discuss the empirical basis of these ideas.

    ReplyDelete
  16. RobertC:

    ===
    Maybe you should define the 'substantial scientific problems'. Controversies,yes. Works in progress, yes. But substantial problems? I've yet to see one here, that you've actually interpreted the evidence for correctly, that presents a falsification of common descent.
    ===

    Falsification?

    It is amazing how consistent is this evolutionary fallacy. Darwin used it and ever since it has key to evolutionary arguments. It shifts the burden away from the evolutionist who is making the claim, and then trades on a false dichotomy between falsification and fact.

    "If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, then my theory would absolutely break down. But I can find out no such case." --C. Darwin.

    ReplyDelete
  17. I think these posts prove CH's point. If all the intelligence that goes into these posts can not come up with a reasonable interpretation of the biological facts, then how unlikely is it that chance by itself can account for the diversity of life. Probability = 0. Therefore all the evidence is against evolution. Evolutionists are just religious science stoppers.

    .

    ReplyDelete
  18. Zachriel"

    ===
    "And all life forms are related to each other though evolution."

    Yes, that has been well-established by science.
    ===

    Actually that has *never* been established. Not once. Even giving evolution all the breaks, and allowing for the uncertainties of a historical process, it has absolutely failed to prove its claims. We can argue about the details of just how badly evolution does on the evidence, but there is no question that evolution is not a scientific fact, or even anywhere remotely close to such a status. Evolutionists universally claim this, but never back it up. Read Jerry Coyne's latest book, as one recent example.

    ReplyDelete
  19. RobertC:

    ===
    CH: "These similar broken genes (the so-called pseudogenes) are found in patterns that do not fit the expected evolutionary pattern. In these cases even evolutionists admit that they are not due to common descent."

    Whaa? Can I buy a link?
    ===

    Uh, what do you mean?

    ReplyDelete
  20. Derick Childress:

    ===
    I believe I did already.

    (i) the footprints are not consistent in size, shape, or stride with any other known animal; rhinos, hippos, lions, hyenas, pandas, kangaroos, polar bears, turtles, antelopes, geese, etc. We of course cannot rule out chupacabras, yetis, dragons, pixies, or centaurs, but that is of no consequence.

    (ii) With a reasonable degree of certainty, one can say that upon finding elephant tracks, it is a fact that elephants were in the area at one point in the past. With more corroborating evidence, such as elephant stool or elephant blood (from an attack) the fact of the elephant's presence can be asserted with a higher and higher degree of certainty.
    ===

    So now let's bring it back to Giberson's claims. Can you provide these two for his case of the pseudogene?

    ReplyDelete
  21. Pedant:

    ===
    These similar broken genes (the so-called pseudogenes) are found in patterns that do not fit the expected evolutionary pattern.

    Any references to the primary literature on that point?
    ===

    Inferred fitness-reducing mutations in pseudogenes that do not align with common descent are not hard to find. I'd be glad to assist you, but I wonder what difference it would make for you? It has never changed anyone's mind before. Such mutations are simply chalked up to convergence.

    ReplyDelete
  22. Hunter:

    Inferred fitness-reducing mutations in pseudogenes that do not align with common descent are not hard to find. I'd be glad to assist you, but I wonder what difference it would make for you?

    Try. Take a chance. Why the diffidence?

    ReplyDelete
  23. I think we'd all like a reference to an example where biologists "admit that they are not due to common descent" or find "Inferred fitness-reducing mutations in pseudogenes that do not align with common descent."

    I really think the biologists here are puzzled at these claims, particularly at the not aligning with common descent part.

    ReplyDelete
  24. RobertC and Pedant:

    ===
    RobertC:
    I think we'd all like a reference to an example where biologists "admit that they are not due to common descent" or find "Inferred fitness-reducing mutations in pseudogenes that do not align with common descent."

    I really think the biologists here are puzzled at these claims, particularly at the not aligning with common descent part.
    ===

    Rationalism is theory-driven, not data-driven. Data that do not align are explained by the appropriate epicycle, filed away and forgotten. This isn't about science. Biologists are not puzzled, evolutionists are puzzled.


    ===
    Pedant:
    Hunter: What difference it would make for you?

    Try. Take a chance.
    ===

    It's all about "chance" with evolutionists. Who knows, says the evolutionist, perhaps those random nerve firings in my head with just happen to enlighten me. Sorry, not going to happen.





    Pseudogene examples:


    1. Wu XW, Muzny DM, Lee CC, Caskey CT., “Two independent mutational events in the loss of urate oxidase during hominoid evolution,” J Mol Evol. 1992 Jan;34(1):78-84.

    Quote: The nonsense mutation (TGA) at codon 107 is, however, more complicated than others. It occurs in the gorilla, the orangutan, and the gibbon, and therefore requires multiple origins of this nonsense mutation.


    2. Inai Y, Ohta Y, Nishikimi M., The whole structure of the human nonfunctional L-gulono-gamma-lactone oxidase gene--the gene responsible for scurvy--and the evolution of repetitive sequences thereon, J Nutr Sci Vitaminol (Tokyo). 2003 Oct;49(5):315-9.

    Quote: Assuming an equal chance of substitution throughout the sequences, the probability of the same substitutions in both humans and guinea pigs occurring at the observed number of positions and more was calculated to be 1.84 x 10-12. This extremely small probability indicates the presence of many mutational hot spots in the sequences.

    ReplyDelete
  25. Cornelius Hunter said...

    Pseudogene examples:

    1. Wu XW, Muzny DM, Lee CC, Caskey CT., “Two independent mutational events in the loss of urate oxidase during hominoid evolution,” J Mol Evol. 1992 Jan;34(1):78-84.

    Quote: The nonsense mutation (TGA) at codon 107 is, however, more complicated than others. It occurs in the gorilla, the orangutan, and the gibbon, and therefore requires multiple origins of this nonsense mutation.


    Oh dear oh dear oh dear..

    Cornelius caught passing on another quote-mined quote from a paper to paint a dishonest and misleading picture of the results:

    "Abstract: Urate oxidase was lost in hominoids during primate evolution. The mechanism and biological reason for this loss remain unknown. In an attempt to address these questions, we analyzed the sequence of urate oxidase genes from four species of hominoids: human (Homo sapiens), chimpanzee (Pan troglodytes), orangutan (Pongo pygmaeus), and gibbon (Hylobates). Two nonsense mutations at codon positions 33 and 187 and an aberrant splice site were found in the human gene. These three deleterious mutations were also identified in the chimpanzee. The nonsense mutation at codon 33 was observed in the orangutan urate oxidase gene. None of the three mutations was present in the gibbon; in contrast, a 13-bp deletion was identified that disrupted the gibbon urate oxidase reading frame. These results suggest that the loss of urate oxidase during the evolution of hominoids could be caused by two independent events after the divergence of the gibbon lineage; the nonsense mutation at codon position 33 resulted in the loss of urate oxidase activity in the human, chimpanzee, and orangutan, whereas the 13-bp deletion was responsible for the urate oxidase deficiency in the gibbon. Because the disruption of a functional gene by independent events in two different evolutionary lineages is unlikely to occur on a chance basis, our data favor the hypothesis that the loss of urate oxidase may have evolutionary advantages."

    Interesting that Cornelius "I'm not a Creationist, honest!!" Hunter pulled his two examples from a piece of BS by John Woodmorappe (Jan Peczkis) at AnswersInGenesis here.

    ReplyDelete
  26. Thorton:

    ===
    Interesting that Cornelius "I'm not a Creationist, honest!!" Hunter pulled his two examples from a piece of BS by John Woodmorappe (Jan Peczkis) at AnswersInGenesis here.
    ===

    Never heard of it. If they figured it out, then good for them.

    ReplyDelete
  27. Cornelius Hunter said...

    Thorton:

    ===
    Interesting that Cornelius "I'm not a Creationist, honest!!" Hunter pulled his two examples from a piece of BS by John Woodmorappe (Jan Peczkis) at AnswersInGenesis here.
    ===

    Never heard of it.


    Sure you didn't. It was pure luck that the two quotes from two different papers you posted above are the exact verbatim ones provided in the 2004 crappy AIG Woodmorappe article on pseudogenes.

    What an amazing coincidence.

    I invite the readers of this thread to view the AIG article here and see this remarkable coincidence for themselves.

    ReplyDelete
  28. Look on the bright side Cornelius. Only two more miracles like the "identical quotes" one above and you'll qualify for sainthood!

    ReplyDelete
  29. Yeesh. Not only did the articles Hunter went for fail to demonstrate evolutionists "admit that they are not due to common descent" or finding "Inferred fitness-reducing mutations in pseudogenes that do not align with common descent," but they are horribly dishonest quotemines.

    Cornelius, I know you have the computer skills to do a GULO gene phylogenetic tree. Why don't you show us how it conflicts with common ancestry?

    Here's some:
    http://pandasthumb.org/archives/2008/05/23/images/GULO_PHYLIP_Tree_Common_names.png
    http://pandasthumb.org/archives/2008/05/24/images/GULO_CLUSTAL_ALIGN_V2.jpg

    ps-I'll give you a hint-Rats were the outlier in that paper, the ones with the mutational hotspots, skewing the results. With more genome sequences, this is clear.

    These data are public, and you could repeat these experiments yourself.

    Or you could keep pulling from AIG. Guess it is a matter of what literature matters to you.

    ReplyDelete
  30. Cornelius Hunter: Actually that has *never* been established.

    Of course common ancestry has been established. The strongest evidence is in the phylogenetic trees constructed from morphological, embryological and molecular data. But there is also substantial fossil data.

    We've attempted to have this discussion before, but even basic discussions of the basic patterns, or the meaning of correlation, have been fruitless. It's like being stuck on the same chapter of the same Bio 101 textbook forever.

    NATIONAL ACADEMY of SCIENCES: "The theory of evolution has become the central unifying concept of biology and is a critical component of many related scientific disciplines. In contrast, the claims of creation science lack empirical support and cannot be meaningfully tested."

    ReplyDelete
  31. RobertC:

    ===
    Yeesh. Not only did the articles Hunter went for fail to demonstrate evolutionists "admit that they are not due to common descent" or finding "Inferred fitness-reducing mutations in pseudogenes that do not align with common descent,"
    ===

    You would think the evolutionist, when challenged, would at least defer to the facts. Particularly when the facts were explained beforehand, he expressed disbelief, and then the facts were presented. You can imagine evolutionists making their silly claims when the facts are not readily apparent. But when the facts are right here in plain sight? Incredibly, this is a typical example of evolutionary thought. Even in such a case the evolutionist continues with the bluster. Rather than read what is presented, acknowledge the facts, and deal with them, evolutionists simply look the other way, in convenient denial, and claim the one who points out evolutionist's silliness has failed. Let's review the facts for all to see:

    ===
    CH: These similar broken genes (the so-called pseudogenes) are found in patterns that do not fit the expected evolutionary pattern. In these cases even evolutionists admit that they are not due to common descent.

    RobertC: I think we'd all like a reference to an example where biologists "admit that they are not due to common descent" or find "Inferred fitness-reducing mutations in pseudogenes that do not align with common descent." I really think the biologists here are puzzled at these claims, particularly at the not aligning with common descent part.

    CH quoting paper: "The nonsense mutation (TGA) at codon 107 is, however, more complicated than others. It occurs in the gorilla, the orangutan, and the gibbon, and therefore requires multiple origins of this nonsense mutation."

    RobertC: Yeesh. Not only did the articles Hunter went for fail to demonstrate evolutionists "admit that they are not due to common descent" or finding "Inferred fitness-reducing mutations in pseudogenes that do not align with common descent," ...
    ===

    The non scientific bluster is really surprising. What is it about "requires multiple origins" that the evolution fails to understand? Or in the other quote provided, what is it about "the same substitutions in both humans and guinea pigs occurring at the observed number of positions and more was calculated to be 1.84 x 10-12. This extremely small probability indicates the presence of many mutational hot spots in the sequences" that the evolution fails to understand?


    ===
    but they are horribly dishonest quotemines.
    ===

    Horribly dishonest? Now the evolution skeptic is the one who is dishonest? Exactly how does that work? What is dishonest about this interchange on my part?


    ===
    Or you could keep pulling from AIG.
    ===

    But I already stated that I didn't pull from AIG. Oh, that's right, I'm dishonest. This is evolutionary thinking in action.

    ReplyDelete
  32. Cornelius Hunter said...

    ===
    Or you could keep pulling from AIG.
    ===

    But I already stated that I didn't pull from AIG. Oh, that's right, I'm dishonest. This is evolutionary thinking in action.


    If not from AIG, then where exactly did you get this quote CH?

    "The nonsense mutation (TGA) at codon 107 is, however, more complicated than others. It occurs in the gorilla, the orangutan, and the gibbon, and therefore requires multiple origins of this nonsense mutation."

    ReplyDelete
  33. CH: "Or in the other quote provided, what is it about "the same substitutions in both humans and guinea pigs occurring at the observed number of positions and more was calculated to be 1.84 x 10-12. This extremely small probability indicates the presence of many mutational hot spots in the sequences" that the evolution fails to understand?"

    Umm, the evolutionist has provided you links on why the paper is wrong. Rats, guinea pigs, and humans were compared in the paper. With more genes from other organisms sequenced, it is abundantly clear rats are the outlier. It is the rat that has evolved significantly from the ancestral sequence, not the Guinea Pig and primate that have converged. The calculation does not apply because the human and guinea pig conserved changes are conserved across other species. The authors had the small probability of human and guinea pig sequences converging right, but came up with the wrong explanation-they came up with mutational hotspots, when the answer was that the sequences were ancestral, and not converged!

    This is clearly explained here, with primary data:
    http://pandasthumb.org/archives/2008/05/the-revenge-of-1.html

    This is the danger of approaching the literature non-critically, picking tidbits found by AIG and trumpeting them as falsifications.

    By the way, genome sequences are publicly available. You could do these analyses yourself. Try it, and tell me what you find so compelling about this pseudogene.

    ReplyDelete
  34. And all life forms are related to each other though evolution. These are important truths that science has discovered through careful research.

    Sometimes I envy the BLIND FAITH of evolutionists.

    ReplyDelete
  35. "Sometimes I envy the BLIND FAITH of evolutionists."

    Ironic, considering the evolutionists are the onces advancing the empirical data over the "Answers in Genesis" based misinterpretation thereof.

    ReplyDelete
  36. RobertC:

    ===
    picking tidbits found by AIG and trumpeting them as falsifications.
    ===

    Why do you say "picking tidbits found by AIG" this when I already corrected you?

    ===
    This is the danger of approaching the literature non-critically
    ===

    I did not approach the literature non-critically.

    ===
    trumpeting them as falsifications.
    ===

    Now you're back to the "falsification" fallacy again. Where did I say this falsified evolution?


    ===
    The authors had the small probability of human and guinea pig sequences converging right, but came up with the wrong explanation-they came up with mutational hotspots, when the answer was that the sequences were ancestral, and not converged!

    This is clearly explained here, with primary data:
    http://pandasthumb.org/archives/2008/05/the-revenge-of-1.html
    ===


    That's fair. My notes predate this blog post by Musgrave (as well as that AIG link). But of course the so-called "hotspots" are not controversial, except I guess with evolutionists.

    ===
    By the way, genome sequences are publicly available. You could do these analyses yourself.
    ===

    I did a fair amount of sequence aligning and analysis of both the GULO and urate oxidate pseudogenes. The comparisons are not nearly as simple and straightforward as you suggest.


    ===
    Try it, and tell me what you find so compelling about this pseudogene.
    ===

    I didn't find anything compelling about it (another strawman of yours?). These pseudogenes do not tell a real obvious story. I have no problem with Musgrave's post about the hotspots. That doesn't change the fact that pseudogenes, like the rest of biology, reveal similarities that are not according to the expected pattern. A fact that you still seem to be in denial about.

    ReplyDelete
  37. Zachriel:

    ===
    Cornelius Hunter: Actually that has *never* been established.

    Of course common ancestry has been established.
    ===

    No it has not.


    ===
    The strongest evidence is in the phylogenetic trees constructed from morphological, embryological and molecular data. But there is also substantial fossil data.
    ===

    That is (i) affirming the consequent and (ii) confirmation bias. For (i), successful predictions do not confirm the theory, except is you are an evolutionist I guess. For (ii), the data are riddled with prediction failures which are not mere "noise." So if you really believed in your method, you would have dropped evolution already.


    ===
    We've attempted to have this discussion before, but even basic discussions of the basic patterns, or the meaning of correlation, have been fruitless. It's like being stuck on the same chapter of the same Bio 101 textbook forever.
    ===

    Your ideas on why the trees prove evolution were like arguments about why epicycles prove geocentrism. On the other hand, if there is a textbook, journal paper, etc, that makes your point, then let's have a look.


    ===
    NATIONAL ACADEMY of SCIENCES: "The theory of evolution has become the central unifying concept of biology and is a critical component of many related scientific disciplines. In contrast, the claims of creation science lack empirical support and cannot be meaningfully tested."
    ===

    There is no doubt that evolutionists make this claim that evolution and common descent are established facts. That is not in question here. The problem is they don't support this rather remarkable claim. So these high claims are nothing more than arguments from authority. In science, we need to evidence, not the bluster.

    ReplyDelete
  38. Cornelius Hunter said...

    RobertC:

    ===
    picking tidbits found by AIG and trumpeting them as falsifications.
    ===

    Why do you say "picking tidbits found by AIG" this when I already corrected you?


    You say a lot of things that turn out not to be true CH.

    My notes predate this blog post by Musgrave (as well as that AIG link)

    Do tell. The AIG article by Woodie dates from Dec 2004. When did you read the papers and make your notes?

    ReplyDelete
  39. "That doesn't change the fact that pseudogenes, like the rest of biology, reveal similarities that are not according to the expected pattern. A fact that you still seem to be in denial about."

    "Not according to the expected pattern."

    We've come a long way from:

    "In these cases even evolutionists admit that they are not due to common descent."

    But regardless, you can't present a single example of a significant unexpected pattern that we'd have to admit is not due to common descent, and I'm supposed to admit my denial, and abandon evolution?

    You present data, and tell me I'm wrong. I show the data is false/misinterpreted, I'm still wrong? Is this moderate empiricism, or are you trying to rationalize your beliefs?

    ReplyDelete
  40. RobertC:

    ===
    "That doesn't change the fact that pseudogenes, like the rest of biology, reveal similarities that are not according to the expected pattern. A fact that you still seem to be in denial about."

    "Not according to the expected pattern."

    We've come a long way from:

    "In these cases even evolutionists admit that they are not due to common descent."
    ===

    A long way? Robert these are synonymous. If identical mutations occur independently then they are (A) Not according to the expected pattern and (B) Not due to common descent. I don't know how I can make this any more clear.

    This denial is just bizarre, but this isn't Robert. This is typical for evolutionists.



    ===
    But regardless, you can't present a single example of a significant unexpected pattern that we'd have to admit is not due to common descent,
    ===

    What happened to the urate oxidase example? Doesn't count?



    ===
    and I'm supposed to admit my denial, and abandon evolution?
    ===

    For the umpteenth time, no one is asking you to abandon evolution, as if that were even remotely possible. The question at hand is Giberson's, and evolution's continual, assertion that common descent is the only explanation for pseudogenes. Rationalists are so wedded to their false dichotomy between the certainty of their theory or its absolute falsification, they are unable to work through the evidence.


    ===
    You present data, and tell me I'm wrong. I show the data is false/misinterpreted, I'm still wrong?
    ===

    You did not show that mutational hotspots are false. You showed that in a *particular* case, there was a personal communication from an author taking back one particular conclusion of hotspots. No problem, that's fine. But that doesn't mean hotspots are a fiction.

    ReplyDelete
  41. CH,
    "What happened to the urate oxidase example? Doesn't count?"

    Hard to say, since the quotation you provided ("The nonsense mutation (TGA) at codon 107 is, however, more complicated than others. It occurs in the gorilla, the orangutan, and the gibbon, and therefore requires multiple origins of this nonsense mutation.") doesn't appear anywhere in the cited paper (Wu et al.1992).

    ReplyDelete
  42. Zachriel: The strongest evidence is in the phylogenetic trees constructed from morphological, embryological and molecular data. But there is also substantial fossil data.

    Hunter: That is (i) affirming the consequent and (ii) confirmation bias. For (i), successful predictions do not confirm the theory, except is you are an evolutionist I guess.

    Successful predictions don't confirm a theory? Tell that to Einstein.

    ReplyDelete
  43. Zach:”The strongest evidence is in the phylogenetic trees constructed from morphological, embryological and molecular data. But there is also substantial fossil data."

    The problem is that word “constructed”, the trees are not observed, you have actual morphological, embriological and molecular data. You do not see the the branches and the junctions, you see only the supposed tree from the top. In the top you draw the nested hierarchies and imagine a tree behind.
    And also the darwinist admits that at the base you do not have the supposed log of the tree but a net where genes jump from one side to other of that net by LGT.

    ReplyDelete
  44. 4afb9302-32ec-11e0-becb-000bcdcb471e said...

    CH,
    "What happened to the urate oxidase example? Doesn't count?"

    Hard to say, since the quotation you provided ("The nonsense mutation (TGA) at codon 107 is, however, more complicated than others. It occurs in the gorilla, the orangutan, and the gibbon, and therefore requires multiple origins of this nonsense mutation.") doesn't appear anywhere in the cited paper (Wu et al.1992).


    Awww, you spoiled my punch line!

    As you note, that quote does not appear in the paper that CH claims. The one he supposedly read and took notes on. It actually came from this paper.

    Loss of Urate Oxidase Activity in Hominoids and its Evolutionary Implications
    Masako Oda, Yoko Satta, Osamu Takenaka, Naoyuki Takahata
    Mol Biol Evol (2002) 19 (5): 640-653.

    "Another nonsense mutation at codon 187 is shared by the human, the chimpanzee and the gorilla, so that it is most likely to have occurred in their ancestral species. The nonsense mutation (TGA) at codon 107 is, however, more complicated than others. It occurs in the gorilla, the orangutan, and the gibbon, and therefore requires multiple origins of this nonsense mutation. Overall, it is remarkable that, except one CGA codon in exon 6, all the other four CGA codons are converted to the TGA termination codon in all or some of the hominoids."

    Cornelius was in such a hurry to sling any mud he could find at evolution that he C&Ped the wrong reference.

    Also as noted, the paper was egregiously quote-mined by Woodmorappe and doesn't come close to supporting Cornelius' original claim.

    Oopsie!

    ReplyDelete
  45. 4afb9302-32ec-11e0-becb-000bcdcb471e: Hard to say, since the quotation you provided ("The nonsense mutation (TGA) at codon 107 is, however, more complicated than others. It occurs in the gorilla, the orangutan, and the gibbon, and therefore requires multiple origins of this nonsense mutation.") doesn't appear anywhere in the cited paper (Wu et al.1992).

    Oda et al., Loss of Urate Oxidase Activity in Hominoids and its Evolutionary Implications, Molecular Biology and Evolution 2002.

    Here's the abstract:
    http://mbe.oxfordjournals.org/content/19/5/640.short

    ReplyDelete
  46. Hunter:

    What is it about "requires multiple origins" that the evolution fails to understand?

    Is this an equivocation about the word "origins"?

    The authors could have said "requires multiple occurrences" just as well.

    ReplyDelete
  47. Cornelius Hunter: That doesn't change the fact that pseudogenes, like the rest of biology, reveal similarities that are not according to the expected pattern.

    You say that, but you provide examples that are consistent with common descent.

    Zachriel: The strongest evidence is in the phylogenetic trees constructed from morphological, embryological and molecular data. But there is also substantial fossil data.

    Cornelius Hunter: That is (i) affirming the consequent and ...

    Confusion on the very basics of the scientific method is why discussions of the particulars of biology are so often unfruitful.

    Affirming the consequent
    if p then q, q, therefore p.

    Hypothesis-testing
    if p then q, q supports p

    The more unexpected the result, the more types of tests, the wider the divergence in methodologies, the stronger that support.

    Cornelius Hunter: For (ii), the data are riddled with prediction failures which are not mere "noise."

    Sorry, but there is a very significant nested hierarchy pattern. It exists, and it won't go away because of any supposed anomalies or misunderstandings on your part.

    Cornelius Hunter: Your ideas on why the trees prove evolution were like arguments about why epicycles prove geocentrism.

    Again, that is incorrect. Geocentrism doesn't make *entailed* predictions about planetary movements. Any point in space can be treated as the center and yield the same results. Compare to the entailed predictions concerning Newtonian Mechanics, such as the retardation of the pendulum.

    Cornelius Hunter: But that doesn't mean hotspots are a fiction.

    Mutations are thought to be random with respect to fitness, but they are not purely random by any means. There may be mutational biases, mutational hotspots, or different rates in different species. None of this calls into question common descent, or evolution generally.

    ReplyDelete
  48. Cornelius Hunter: If identical mutations occur independently then they are (A) Not according to the expected pattern and (B) Not due to common descent. I don't know how I can make this any more clear.

    There are only four bases. Across a large genome, it is quite easy to find random substitutions that are identical due to chance alone. If there are mutational biases, then the chances are even greater.

    ReplyDelete
  49. Zach"Hypothesis-testing
    if p then q, q supports p"

    That is wrong. AT least in my world.

    ReplyDelete
  50. Blas said...

    Zach"Hypothesis-testing
    if p then q, q supports p"

    That is wrong. AT least in my world.


    That says more about your world than it does about hypothesis testing.

    ReplyDelete
  51. Blas said...

    Zach"Hypothesis-testing
    if p then q, q supports p"

    That is wrong. AT least in my world.


    And yet we all use inductive reasoning every day, usually without realizing it.

    ReplyDelete
  52. Science 101- Lesson #1

    How evolution differs from other sciences (C02 climate predictions excluded).

    Rather than critically look at exceptions and flukes in their findings as problems with their theory, they are quick to answer these problems with almost willy-nilly answers. They are in a constant search to cherry pick evidence that could, may, possibly lend support to their theory. Whatever could, may, possibly lend support is hyped and milked for every ounce they can imagine its worth (i.e. missing link fiasco's, etc).

    Next, let's look at how real science is performed.

    ReplyDelete
  53. CH in quotes:

    "If identical mutations occur independently then they are (A) Not according to the expected pattern and (B) Not due to common descent. I don't know how I can make this any more clear. This denial is just bizarre, but this isn't Robert. This is typical for evolutionists."

    LOL. You kill me. Of course if mutations occur independently (after the last common ancestor) they are not due to common ancestry! This is absurd! But you pile on the rhetoric, and we're suddenly to:

    "These similar broken genes (the so-called pseudogenes) are found in patterns that do not fit the expected evolutionary pattern. In these cases even evolutionists admit that they are not due to common descent. "

    So the evolutionists admission is the changes that occur after divergence from a common ancestor aren't due to common ancestry? Rhetorical gymnastics, designed to appear as if you are saying evolutionary biologists are admitting something is wrong with common descent.

    But my main objection here is to "expected pattern." What is the expected pattern? I'd say substitutions that neatly align to understood phylogeny, with some changes after divergence from a common ancestor. I'd also say there is NO example you've provided that violated the expected pattern in any substantial way.

    "What happened to the urate oxidase example? Doesn't count?"

    Well, until this morning there was no REAL reference. At any rate, the paper shows really nice patterns of substitution across the primate UOX pseudogene. Almost all (of many changes) align with known primate phylogeny. One substitution appears in gibbons, orangutans and gorillas, but not humans and chimps (if you believe the sequence data-it is quite old, and BLAST shows some gorilla sequences without the substitution). Regardless, this suggests two events, like the change being present in an ancestor, and reverted in the human/chimp lineage. 1 of 4 bases, unconstrained, long times. Not that improbable. Does a .1% minor mystery falsify the other 99.9%?

    "You did not show that mutational hotspots are false. You showed that in a *particular* case, there was a personal communication from an author taking back one particular conclusion of hotspots. No problem, that's fine. But that doesn't mean hotspots are a fiction."

    When did I argue for or against mutational hotspots? I merely pointed out the authors were wrong to claim mutational hotspots in humans and guinea pigs, when additional sequences clearly show rats were an outlier. This renders the big number calculation for the convergence of human and guinea pig meaningless. That is all. Not trying to disprove hotspots.

    ReplyDelete
  54. Pedant:

    ===
    Hunter: What is it about "requires multiple origins" that the evolution fails to understand?

    Is this an equivocation about the word "origins"?
    ===

    No.

    ===
    The authors could have said "requires multiple occurrences" just as well.
    ===

    Makes no difference. "Origins", "occurrences", pick your favorite word.

    ReplyDelete
  55. One more note:

    Because there are only 4 bases, and DNA sequencing makes mistakes, molecular phylogeny is not based on eyeballing single bases. It is a statistical science.

    You will always win the "violates a pattern" argument if you scour the literature for single bases in 20 year old sequences.

    Now, do a phylogeny for me with say, good bootstrap values that breaks the mold, and we'll talk.

    Data and methodology is publicly available:

    http://www.soe.ucsc.edu/classes/bme110/Winter09/Lectures/BME110-Lect8.Feb17.print.pdf

    ReplyDelete
  56. Blas: The problem is that word “constructed”, the trees are not observed, you have actual morphological, embriological and molecular data.

    So are elliptical orbits. So?

    Blas: And also the darwinist admits that at the base you do not have the supposed log of the tree but a net where genes jump from one side to other of that net by LGT.

    Indeed, there is substantial horizontal gene flow even in modern organisms. Again, so?

    Zachriel: Hypothesis-testing
    if p then q, q supports p


    Blas: That is wrong. AT least in my world.

    It's the basis of the scientific method, hypothetico-deduction. Let's take an example. Newton proposed laws of gravity and motion. Halley took those laws and applied them to cometary data. He determined that certain of those comets were actually the same body, and he predicted when and where that comet would reappear. The comet was observed in the predicted quadrant on Christmas night, 1758. The observation provided dramatic support, something the entire world could see, but it didn't "prove" Newton's Laws.

    ReplyDelete
  57. Teford:

    Science 101- Lesson #1

    How evolution differs from other sciences (C02 climate predictions excluded).


    How about that? A science-ignorant pastor is lecturing us on science.

    Chalk one up for hubris on Tedford's list of deadly sins. Looks like you're gonna be holding hands with your colleague Ted Haggard in the lake of fire.

    And why am I not surprised you're a AGW-denialist?

    ReplyDelete
  58. Neal,

    1) Are paternity tests a reliable indicator of relatedness? If a paternity test returns a positive result, is that a reliable indicator that the two people tested are closely related?

    Lest you think I'm trying to 'trick' you in some way, feel free to ask me any number of yes/no questions yourself.

    ReplyDelete
  59. What exactly is the mechanism for HGT in modern multicellular organisms? Has it been observed or just inferred?

    ReplyDelete
  60. RobertC:

    Fair point about the OP. More explanation is needed.

    ===
    But my main objection here is to "expected pattern." What is the expected pattern? I'd say substitutions that neatly align to understood phylogeny, with some changes after divergence from a common ancestor. I'd also say there is NO example you've provided that violated the expected pattern in any substantial way.

    Not that improbable. Does a .1% minor mystery falsify the other 99.9%?
    ===

    That's not the issue. That is, the question is not whether or not there are similarities, genetic and otherwise, between species. The evolutionary argument is that there are similarities that don't make sense which myteriously are identical between cousin species. An obvious and compelling sign of common descent.

    The pseudogenes provided a great example of this, and are commonly used, such as by Giberson. But inferred mutation events sometimes are not homologous. In those cases even evolutionists agree they are not due to common descent. And these cases show up on pseudogenes. Urate oxidase has several. And sometimes they are debilitating. So the evolutionary argument amounts to special pleading.

    In other words, when such mutations are found in pseudogenes that align with common descent, then they are declared to be compelling proof texts for common descent. But when they do not align with CD, then such mutations are simply explained by common mechanism. This is special pleading. If a mutation (that doesn't align with CD) can be explained by common mechanism, then mutations that do align with CD can also be explained by common mechanism.

    ===
    That is all. Not trying to disprove hotspots.
    ===

    OK, good.

    ReplyDelete
  61. Nat, look here for starters. Is it really so hard to do a little research on your own? What do you tell your students if they ask where to find information on a certain subject?

    ReplyDelete
  62. natschuster: What exactly is the mechanism for HGT in modern multicellular organisms?

    Horizontal gene flow is most prevalent in single-celled organisms, such as through conjugation. Bacteria will even pick up stray pieces of DNA from the environment.

    As for multicellular organisms, hybridization is not uncommon, especially in plants. Retroviruses are another mechanism, whereby a virus becomes incorporated into a cell's genome. If this occurs in a germ cell, then it can be transmitted to new generations.

    ReplyDelete
  63. I know hybridization has been observed. But usually works only in closely related species. And would retroviruses be able to, for example, get dog DNA into a cat, or do they only get virus DNA into the host species.

    ReplyDelete
  64. Troy:

    I looked at the article you linked. It talked a lot about bacteria and articifial gene transfer. What I'm asking about is how do we get dog DNA into a cat by natural means.

    ReplyDelete
  65. The evidence indicates that genetic transfer is rare between distantly related animals, though may be more common in aquatic organisms. Plants are more prone to distant hybrids.

    ReplyDelete
  66. Nat, what makes you think there's dog DNA in cats?

    ReplyDelete
  67. Zach:"So are elliptical orbits. So?"

    You can measure the position of the planets for each day during a rotation around the sun, you do not have the animals or plant to fill the branches of the tree.

    "Indeed, there is substantial horizontal gene flow even in modern organisms. Again, so?"

    Then you do not ahve a tree of life you have net, then you can prove the unique common ancestor.


    "The observation provided dramatic support, something the entire world could see, but it didn't "prove" Newton's Laws."

    Exactly, q do not support p. p stands because q.
    There is no number of q will prove p.

    ReplyDelete
  68. CH,
    "In other words, when such mutations are found in pseudogenes that align with common descent, then they are declared to be compelling proof texts for common descent. But when they do not align with CD, then such mutations are simply explained by common mechanism. "

    you are ignoring Robert's point that you have to look at the total data. when 99% of the data fit the predicted pattern (as is true for pseudogenes and other data), you say your hypothesis is supported. the 1% is certainly interesting, and should be explored further, but a 100% fit is not even expected, esp. in biology. or does the fact that 1 out of 10 dentists doesn't recommend sugar-free gum convince you to chew Bubblicious?

    ReplyDelete
  69. "But inferred mutation events sometimes are not homologous."

    Right

    "In those cases even evolutionists agree they are not due to common descent."

    Because they can't be by definition (post-common ancestor). Naively, someone might misconstrue your statement implies a failure of evolutionary biology.

    "And these cases show up on pseudogenes. Urate oxidase has several."
    And sometimes they are debilitating."

    Debilitating? This is a pseudogene, and "..... the inactivation of the gene in the clade of the human and the great apes results from a single CGA to TGA nonsense mutation in exon 2..." This is not position 107 in exon 3, which you quoted, where a difference was seen, so I'm at a loss at to where fitness would come into this.

    "So the evolutionary argument amounts to special pleading."

    Special pleading would be arguing one substitution matters where another does not, all things being equal. Sort of like harping on position 107 as some sort of problem for evolution-it is choosing the 0.1% exception vs. the rest of the data, with no justification.

    Drawing a statistics-based conclusion based on the patterns of substitutions across this and other genes is not. Again, with only 4 bases, reversions can occur. Sequencing errors can occur, or polymorphism in the ancestral species. Thus, the statistical science of molecular phylogeny.

    So, concluding all great apes share a broken gene (apparently broken at the same position), is not special pleading. And as you say, these pseudogenes are "myteriously are identical between cousin species. An obvious and compelling sign of common descent."

    ReplyDelete
  70. Blas: You can measure the position of the planets for each day during a rotation around the sun, ...

    The ellipse is a construction, just like the nested hierarchy.

    Blas: ... you do not have the animals or plant to fill the branches of the tree.

    You're confusing the nested hierarchy (observed) with the phylogenetic tree (inferred). We can discuss the latter, but not when you deny the former.

    Blas: Exactly, q do not support p. p stands because q. There is no number of q will prove p.

    Q never "proves" p. It supports it or falsifies it. If you prefer, q shows the consistency of p with the evidence. However, strong predictions can offer significant support — unless you are saying that the sighting of Halley's comet didn't support his hypothesis. Lucky guess, that.

    ReplyDelete
  71. Zach:"Blas: You can measure the position of the planets for each day during a rotation around the sun, ...

    The ellipse is a construction, just like the nested hierarchy.

    Blas: ... you do not have the animals or plant to fill the branches of the tree.

    You're confusing the nested hierarchy (observed) with the phylogenetic tree (inferred). We can discuss the latter, but not when you deny the former."

    I always was talking about the tree, why are you bringing the nested hierarchy now? I said you observe it looking the tree from the top.

    "unless you are saying that the sighting of Halley's comet didn't support his hypothesis. Lucky guess, that."

    Maybe the problem is the meaning of the word "support". A hypotesis well supported is a truth? at least a scientific truth?

    ReplyDelete
  72. natschuster said...

    What exactly is the mechanism for HGT in modern multicellular organisms? Has it been observed or just inferred?


    Seems to me you asked this same question about a month ago, and it was answered a month ago.

    I guess you were too busy cutting pages out of textbooks so your students wouldn't be exposed to scientific ideas that contradict your religious beliefs.

    What will be the next topic you deny your students knowledge of? Radiometric dating? Hominid fossils? I'm sure your list must be long.

    ReplyDelete
  73. Blas: I always was talking about the tree, why are you bringing the nested hierarchy now?

    That's fine.

    In any case, you have to start with the observed pattern, the nested hierarchy. You would still need to understand hypothesis-testing, though.

    Blas: Maybe the problem is the meaning of the word "support". A hypotesis well supported is a truth?

    It means that you can get on a plane and reliably fly across oceans.

    Blas: at least a scientific truth?

    Eppur si muove.

    ReplyDelete
  74. 4afb9302-32ec-11e0-becb-000bcdcb471e said...

    CH,
    "In other words, when such mutations are found in pseudogenes that align with common descent, then they are declared to be compelling proof texts for common descent. But when they do not align with CD, then such mutations are simply explained by common mechanism. "

    you are ignoring Robert's point that you have to look at the total data. when 99% of the data fit the predicted pattern (as is true for pseudogenes and other data), you say your hypothesis is supported. the 1% is certainly interesting, and should be explored further, but a 100% fit is not even expected, esp. in biology. or does the fact that 1 out of 10 dentists doesn't recommend sugar-free gum convince you to chew Bubblicious?


    Cornelius is just following the standard Creationist playbook:

    1. Examine a large collection of data, find a few outliers.
    2. Ignore the explanation for the outliers.
    3. Scream bloody murder that all the data must be wrong because of the outliers.

    Cornelius doesn't seem to be savvy enough to freelance his own anti-science attacks. It's standard Creto Rhetoric 101 the whole way.

    ReplyDelete
  75. Troy and Thorton:

    The article posted did say that there was fungus DNA in a plant. I'm asking how it got there. I couldn't find any mention of a plausible mechanism. Dogs and cats was just an example.

    And I taught radiometric dating. I even came up with an effective way to teach the concept to leanring disabled kids. (I used jelly beans.) The problem I had with Haeckel's drawing was the fact that they were, at best, wildly inaccurate, if not actually fraudulent. I didn't skip the pages in the textbooks that had photographs instead of the drawings. Though I did mention that the embryos are different at the blastula stage, and at gastrulization, just for the sake of accuracy and balance.

    ReplyDelete
  76. Correction:

    The fungus DNA is actually in an aphid. Sorry, my bad.

    ReplyDelete
  77. Zach:"Blas: Maybe the problem is the meaning of the word "support". A hypotesis well supported is a truth?

    It means that you can get on a plane and reliably fly across oceans."

    That is not truth, what make me get a plane to reliably fly is not the Newton´s theory, but the tested aplication of it. If we never get the dark matter, the plane will fly again and the Newton´s theory will be wrong.


    Blas: at least a scientific truth?

    Eppur si muove.

    That is not an answer.

    ReplyDelete
  78. Blas: That is not truth, what make me get a plane to reliably fly is not the Newton´s theory, but the tested aplication of it.

    Newton's Theory isn't judged by some measure of philosophical truth, but its fit to the evidence, its reliability at making empirical predictions.

    Blas: at least a scientific truth?

    Galileo thought the scientific evidence supported the motion of the Earth, so he was speaking the truth as he knew it when he uttered "Eppur si muove", but falsely when he abjured to the Inquisition.

    ReplyDelete
  79. These similar broken genes (the so-called pseudogenes) are found with broken parts that do not fit the expected evolutionary pattern. In these cases even evolutionists admit that the breaks are not due to common descent. It is therefore the fallacy of special pleading to claim that when such breaks fit the expected evolutionary pattern they serve as proof texts for evolution.

    So, in support of the above, Hunter came up with two classic creationist arguments with literature references from AIG. And those arguments have now been roundly discredited.

    Surely there must be many, many more examples of sequences not fitting common descent in the vast and growing genomic databases available online and elsewhere. That represents a challenge and an opportunity for Hunter (or one of his acolytes) to storm those peer-reviewed publication ramparts and BLAST evolution to the dustbin of history.

    Isn't that what a motivated empiricist would do?

    ReplyDelete
  80. nano:

    ===
    you are ignoring Robert's point that you have to look at the total data. when 99% of the data fit the predicted pattern (as is true for pseudogenes and other data), you say your hypothesis is supported. the 1% is certainly interesting, and should be explored further, but a 100% fit is not even expected, esp. in biology. or does the fact that 1 out of 10 dentists doesn't recommend sugar-free gum convince you to chew Bubblicious?
    ===

    No, I'm not ignoring that point. I'm not pointing to a couple of homoplasies and claiming the CD model therefore fails.

    The evolutionary argument is that there are similarities that don't make sense (ie, shared errors) which myteriously are identical between cousin species. An obvious and compelling sign of common descent.

    What I am pointing out is that this argument amounts to special pleading. Why? Because there are shared errors that are not homologous. They are homoplasies. Evolutionists say they were produced by identical, indendent events (common mechanism). It is special pleading to turn around and explain the ones that are homologous as such powerful evidence. Without first presupposing evolution, one could just as easily explain those also by common mechanism.

    ReplyDelete
  81. Pendant-

    I'm sure we'll be hearing about the "problems" of evolution for years to come, despite the huge amount of data and excellent statistics in papers like:

    A molecular phylogeny of living primates.
    PLoS Genet. 2011 Mar;7(3):e1001342. Epub 2011 Mar 17.
    http://www.ncbi.nlm.nih.gov/pubmed/21436896


    Comparative genomic analyses of primates offer considerable potential to define and understand the processes that mold, shape, and transform the human genome. However, primate taxonomy is both complex and controversial, with marginal unifying consensus of the evolutionary hierarchy of extant primate species. Here we provide new genomic sequence (∼8 Mb) from 186 primates representing 61 (∼90%) of the described genera, and we include outgroup species from Dermoptera, Scandentia, and Lagomorpha. The resultant phylogeny is exceptionally robust and illuminates events in primate evolution from ancient to recent, clarifying numerous taxonomic controversies and providing new data on human evolution. Ongoing speciation, reticulate evolution, ancient relic lineages, unequal rates of evolution, and disparate distributions of insertions/deletions among the reconstructed primate lineages are uncovered. Our resolution of the primate phylogeny provides an essential evolutionary framework with far-reaching applications including: human selection and adaptation, global emergence of zoonotic diseases, mammalian comparative genomics, primate taxonomy, and conservation of endangered species.

    ReplyDelete
  82. This comment has been removed by the author.

    ReplyDelete
  83. CH,
    "What I am pointing out is that this argument amounts to special pleading. Why? Because there are shared errors that are not homologous. They are homoplasies."

    Of course. but the vast majority are homologous. if the the situation was reversed and homoplasies vastly outnumbered homologies (or even if they were more evenly distributed) you would have a point. but they don't and you don't.

    "It is special pleading to turn around and explain the ones that are homologous as such powerful evidence. Without first presupposing evolution, one could just as easily explain those also by common mechanism. "

    no. convergence is mathematically much less likely to occur than inheritance through common descent.

    ReplyDelete
  84. RobertC, it would kill Hunter to even consider the possibility that humans share a common ancestor with all those other primates.

    Where would that leave Adam and Eve?

    ReplyDelete
  85. I'm puzzled by the use of 'common mechanism.'

    There are many causes of gene mutation. The cause of an A->T conversion in one organism need not be the same in another organism. Nor is it the same as a T->A reversion that might give the appearance of misgrouping by species at a single position.

    Further, the numbers are relevant. A reversion, for example, capable of causing the same base (1/4) to appear at a single position seems not at all improbable.

    However, If multiple positions follow such a pattern, things become less probable-here the guinea pig math you cited above actually would apply! By the time we reach the 99.9% of bases that follow a pattern-the odds are exceedingly low of all of them independently aligning without common ancestry. So, if you can dismiss common descent, and have a "common mechanism" to explain such low probabilities, then please, describe this mechanism and how it overcomes insurmountable odds.

    Until then, can we take common descent as the only reasonable model that fits the phylogenetic data like in the paper I've presented above?

    ReplyDelete
  86. RobertC:

    ===
    "But inferred mutation events sometimes are not homologous."

    Right

    "In those cases even evolutionists agree they are not due to common descent."

    Because they can't be by definition (post-common ancestor). Naively, someone might misconstrue your statement implies a failure of evolutionary biology.
    ===

    Right. I agree more explanation is needed.


    ===
    Debilitating? This is a pseudogene, and "..... the inactivation of the gene in the clade of the human and the great apes results from a single CGA to TGA nonsense mutation in exon 2..." This is not position 107 in exon 3, which you quoted, where a difference was seen, so I'm at a loss at to where fitness would come into this.
    ===

    That quote illustrates the similarities that are non homologous, that's all. There are several such examples in urate oxidase across the primates. In fact some must have occurred more than merely twice. An identical 8 residue segment is inferred to have inserted independently. An exon 2 nonsense mutations is thought to have occurred independently multiple times. An exon 3 nonsense mutation is inferred to have occurred independently, multiple times. These are low probability events that call for common mechanism.



    ===
    "So the evolutionary argument amounts to special pleading."

    Special pleading would be arguing one substitution matters where another does not, all things being equal. Sort of like harping on position 107 as some sort of problem for evolution-it is choosing the 0.1% exception vs. the rest of the data, with no justification.

    Drawing a statistics-based conclusion based on the patterns of substitutions across this and other genes is not. Again, with only 4 bases, reversions can occur. Sequencing errors can occur, or polymorphism in the ancestral species. Thus, the statistical science of molecular phylogeny.

    So, concluding all great apes share a broken gene (apparently broken at the same position), is not special pleading. And as you say, these pseudogenes are "myteriously are identical between cousin species. An obvious and compelling sign of common descent."
    ===

    Right, but there are breaks that are not homologous.You can argue the multiple, identical mutations constitute low probability events that just happened anyway. Or (more plausibly) you can look for common mechanism. But either way, you are explaining them without CD. So to then pick out other such breaks as evidence of the so-called "shared error" proof, is special pleading.

    ReplyDelete
  87. nano:

    ===
    Of course. but the vast majority are homologous. if the the situation was reversed and homoplasies vastly outnumbered homologies (or even if they were more evenly distributed) you would have a point. but they don't and you don't.
    ===

    No, common mechanism (CM) can explain a prevalence of homologous mutations (though pseudogenes are not as clean as you make it sound). Indeed, the hypothetical you describe (homoplasies vastly outnumbered homologies) I think would be difficult to explain.

    ReplyDelete
  88. CH,
    "common mechanism (CM)" is this the long-awaited glimmer of an alternative hypothesis? please do tell more.

    ReplyDelete
  89. Cornelius Hunter said...

    nano:

    ===
    Of course. but the vast majority are homologous. if the the situation was reversed and homoplasies vastly outnumbered homologies (or even if they were more evenly distributed) you would have a point. but they don't and you don't.
    ===

    No, common mechanism (CM) can explain a prevalence of homologous mutations (though pseudogenes are not as clean as you make it sound). Indeed, the hypothetical you describe (homoplasies vastly outnumbered homologies) I think would be difficult to explain.


    LOL! Ain't Cornelius cute?

    He took the Intelligent Design Creationist argument "common design can explain it" and changed it to "common mechanism can explain it"

    Maybe "CM" will be his big contribution to the ICD movement, like Behe's "IC" and Dembski's "CSI".

    Tell us Cornelius, what observations couldn't be explained by "common mechanism"?

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  90. This comment has been removed by the author.

    ReplyDelete
  91. Quotes from natschuster

    The problem I had with Haeckel's drawing was the fact that they were, at best, wildly inaccurate, if not actually fraudulent.

    No need to skip them. Explain them in their historical context, informed by real scholars.
    For "balance" on this, check Gould and Richardson's works on the subject:
    http://ncseweb.net/creationism/analysis/icon-4-haeckels-embryos (NCSE review)
    http://home.uchicago.edu/~rjr6/articles/Haeckel--fraud%20not%20proven.pdf (paper by Richardson citing many papers by Gould)

    I didn't skip the pages in the textbooks that had photographs instead of the drawings.

    Good.

    Though I did mention that the embryos are different at the blastula stage, and at gastrulization, just for the sake of accuracy and balance.

    That's not "balance". It doesn't contradict evolutionary theory. There's nothing to balance against. I once gave you a link to an article about the hourglass model of animal development. You should really check that out.

    ReplyDelete
  92. "You can argue the multiple, identical mutations constitute low probability events that just happened anyway."

    And depending on how 'multiple' these events are, I don't think the probability is so low.

    "Or (more plausibly) you can look for common mechanism."

    I'm not sure what this 'common mechanism' you are referencing is. Especially in the context or explaining away multiple homologous mutations. Could you elaborate? Is common mechanism an alternative to common descent? Can you give an example of a common mechanism.

    "But either way, you are explaining them without CD."

    No, actually all my explanations have referenced common descent. A common ancestor could contain a change which a sub-lineage reverts back, giving the appearance of mis-grouping species on that gene tree.
    Is this without common descent?

    A ancestral population might not be fixed at a certain position (insertion of 6 bases). Some descendent species (gorilla, orangutan) fix the insertion, which others fix the non-inserted allele. Is this without common descent?

    What explanation for an unusual substitution patterns has been made outside the framework of common descent?

    "So to then pick out other such breaks as evidence of the so-called "shared error" proof, is special pleading."

    Statistics. See above. It isn't cherry-picking, it is observation of the bulk of the data that supports the hypothesis.

    ReplyDelete
  93. Quotes from natschuster

    And would retroviruses be able to, for example, get dog DNA into a cat... [?]

    Yes.

    What exactly is the mechanism for HGT in modern multicellular organisms? Has it been observed or just inferred?

    Other mechanisms involve parasitic or endosymbiotic bacteria, like Wolbachia... actually, better check the introduction of this paper, it's well-referenced .

    http://vsites.unb.br/ib/cel/microbiologia/tebm/wol4.pdf

    ReplyDelete
  94. Robert C said:

    Ironic, considering the evolutionists are the onces advancing the empirical data over the "Answers in Genesis" based misinterpretation thereof.

    What 'empirical' data....biased assumptions and smoke and mirrors???

    ReplyDelete
  95. Geoxus:

    That article explains bacteria genes in fruit flies. What about fungus genes in aphids?

    ReplyDelete
  96. natschuster: What about fungus genes in aphids?

    What about them? Fungi will invade animal cells in order to ingest nutrients. This close proximity can lead to lateral transfer. Many transfers are probably neutral, and just become genomic detritus, but others may provide an advantage. Such transfers will show as an anomaly against the background nested hierarchy pattern.

    ReplyDelete
  97. Science 101. Lesson #2

    Evolution differs from other fields of science (excepting C02 based climate predictions) in its lack of self-disciple to consistently follow a true scientific methodology. The willy nilly evolutionist posts on this article that are presented as matter-of-fact dogma are a case in point.

    Compare the willy nilly posts here explain the myriad of exceptions with this piece of recent news from the field of physics...

    TITLE: New subatomic particle: real or anomaly?

    http://www.msnbc.msn.com/id/42497555/ns/technology_and_science-science/


    "The catch is, the pattern could represent a real physical phenomenon, or it could be a statistical anomaly. Scientists say there's a 1 in 1,000 chance the finding is just a fluke. To get a better idea of whether the signal is real, researchers need to sort through more data.

    Inside the Tevatron, protons and their antimatter partners, antiprotons, are accelerated in a giant ring until they crash into each other at near the speed of light. In the ensuing explosions, many different combinations of exotic particles are created.

    The new result, found at the Tevatron's Collider Detector at Fermilab (CDF), hinges on detecting a couple of hundred extra, unexpected instances of a particular combination of products. Such a finding could indicate that an unknown particle is being created in these collisions."

    Compare this to the uber-hype that was presumptuously generated by the most recent "missing link" or Tiktaalik roseae five years ago. Science appears to be a self policing endeavor, but in the case of evolution and C02 climate predictions the fox is guarding the hen house.

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  98. Here's a link from Discovery.org (which evolutionists hate), but it is an interesting review of Evolutionist Lynn Margulis skepticism of neo-Darwinism. Margulis is calling a spade and spade, which is what science is all about.

    While the evolutionists on this blog are repeating the party line sound bites as if they were "well-established" settled science, behold all is not well in Darwin's house. Even the foxes are revolting!

    The various mechanisms of evolution that you guys proclaim as well established by science, are being challenged by Margulis. Not just the minor points, but the very foundation of neo-Darwinism. Some of the points I have been asking you guys to seriously think through.

    Margulis quoted: "This is the issue I have with neo-Darwinists: They teach that what is generating novelty is the accumulation of random mutations in DNA, in a direction set by natural selection. If you want bigger eggs, you keep selecting the hens that are laying the biggest eggs, and you get bigger and bigger eggs. But you also get hens with defective feathers and wobbly legs. Natural selection eliminates and maybe maintains, but it doesn't create.... [N]eo-Darwinists say that new species emerge when mutations occur and modify and organism. I was taught over and over again that the accumulation of random mutations led to evolutionary change-led to new species. I believed it until I looked for evidence."


    Here's the link:

    http://www.evolutionnews.org/2011/04/lynn_margulis_criticizes_neo-d045691.html


    Margulis should give you guys something to chew on for a long time.

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  99. "What 'empirical' data....biased assumptions and smoke and mirrors???"

    The empirical data I presented here is 8 megabases of new sequence, on top of the completed primate genomes, aligned into a robust phylogeny with excellent statistics.

    A molecular phylogeny of living primates.
    PLoS Genet. 2011 Mar;7(3):e1001342. Epub 2011 Mar 17.
    http://www.ncbi.nlm.nih.gov/pubmed/21436896

    "Compare the willy nilly posts here explain the myriad of exceptions with this piece of recent news from the field of physics..."

    Odd choice. This is a three-sigma finding, which fails to cross the threshold of five sigma that the field sets. That's this line: "Scientists say there's a 1 in 1,000 chance the finding is just a fluke."

    Contrast this to the paper I presented, with very robust statistics (bootstrap and others).

    "Tiktaalik roseae five years ago"

    What's your problem with Tiktaalik?

    ReplyDelete
  100. Neal Tedford: Margulis quoted: "I was taught over and over again that the accumulation of random mutations led to evolutionary change-led to new species. I believed it until I looked for evidence."

    Margulis earned her PhD in 1963 (UC Berkeley), and was in college when the discovery of DNA was still a novelty. She is still fighting the battles of her youth. Science has moved on from simplistic models of mutation and selection.

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  101. ... the discovery of {the structure of} DNA ...

    ReplyDelete
  102. Zachriel, Margulis also said in the same article that "evolutionary biologists believe the evolutionary pattern is a tree. It's not."

    ---

    Zachriel, That's certainly a mighty blow to your starboard bow.

    Your argument against her is because she is too old!!!

    Someone could not make this stuff up.

    She maybe old, but she obviously struck a nerve!

    ReplyDelete
  103. Tedford the shameless charlatan:

    Compare this to the uber-hype that was presumptuously generated by the most recent "missing link" or Tiktaalik roseae five years ago.

    A bigger hype than the search for the Higgs boson, aka the "God particle"? I get twice as many Google hits for "god particle" than for "tiktaalik", and 6 times as many for "higgs boson".

    Don't you ever get tired of lying for Jebus?

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  104. Neal,

    Margulis was right on endosymbiont theory. This earned her acclaim. She also believes HIV doesn't cause AIDS, is a 9/11 truther, and pushed such lousy articles into PNAS that the journal banned communicated submissions by PNAS members.

    So she's entitled to her opinions, but I'd take them with a grain of salt.

    ReplyDelete
  105. RobertC said...

    Neal,

    Margulis was right on endosymbiont theory. This earned her acclaim. She also believes HIV doesn't cause AIDS, is a 9/11 truther, and pushed such lousy articles into PNAS that the journal banned communicated submissions by PNAS members.

    So she's entitled to her opinions, but I'd take them with a grain of salt.


    What RobertC said. Margulis made some very important contributions to science early in her career, but since then has gone farther and farther off the track. Some of the stuff he espouses now is just plain nutty, like the HIV/AIDS denier stuff.

    Tara Smith has a good write up of Margulis' going off the deep end here:

    Margulis does it again

    Being right in one area (symbiogenesis) doesn't make her correct in all areas.

    ReplyDelete
  106. Neal Tedford: Margulis also said in the same article that "evolutionary biologists believe the evolutionary pattern is a tree. It's not."

    Evolutionary biologists are quite aware of the many exceptions to the nested hierarchy. Again, she is fighting old battles. Science has moved on.

    ReplyDelete
  107. Thorton: Being right in one area (symbiogenesis) doesn't make her correct in all areas.

    Quite so. Darwin made huge contributions to biology, and was a very careful observer and researcher. But Pangenesis, his 'provisional hypothesis' of inheritance, was more a bad guess than a theory based on evidence.

    ReplyDelete
  108. Anyone else waiting to hear what "common mechanism" is?

    ReplyDelete
  109. RobertC said...

    Anyone else waiting to hear what "common mechanism" is?


    Cornelius is probably madly searching AIG even as we type.

    ReplyDelete
  110. Robert C: Anyone else waiting to hear what "common mechanism" is?

    Sure are!

    ReplyDelete
  111. natschuster,

    Sorry, I liked to the wrong paper. This is the right one:

    http://www.pnas.org/content/105/44/17023.full

    It doesn't say much, but cites many references with different examples for different mechanisms.

    What about fungus genes in aphids?

    Thorton explained it.

    In cases of parthenogenetic reproduction, Buchnera cells are transferred into the parthenogenetic blastoderm-stage embryos; Buchnera are localized proximal to the host germ cells during early development of the host. Moreover, in cases of sexual reproduction, Buchnera enter sexual eggs at the pre-cellularization stage; at this stage, there are no membranous barriers between Buchnera and the germ lines [14,15]. Such localization of Buchnera cells proximal to host germ lines might provide opportunities for the LGT from Buchnera into the germ lines.

    From the paper:
    http://www.biomedcentral.com/1741-7007/7/12

    I didn't know about that. I just did a Google Scholar search.

    ReplyDelete
  112. Anyone else waiting to hear what "common mechanism" is?

    I bet it involves an intelligently designed algorithm for simulating common ancestry.

    ReplyDelete
  113. Jerry Coyne has a nice post on horizontal gene transfer, including a link to a free recent Current Biology "primer" on the subject.

    here

    ReplyDelete
  114. Margulis is a crackpot, apparently more interested in boosting her own ego than science.

    Among her most crazy claims: her "theory" that sperm tails derive from spirochete bacteria was rejected - not because of lack of evidence, no siree - but because men (the male variety of humans) don't like the idea that part of their sperm is bacterial in origin.

    Yeah, an orgasm (I hope this word is not on the black list) just isn't the same knowing that.

    ReplyDelete
  115. Zachriel,

    Margulis is member of the National Academy of Sciences. The same organization you quoted in a post on April 11 to argue your position from authority.

    So, only those members who are under a particular age can be used for your arguments from authority?

    Do you have something against old people?

    ---

    Also, its good to see that your moving in the right direction concerning nested hierarchies. Yes, there are, as you say, "many exceptions" to the nested hierarchy. Are you ready to embrace the web pattern of life and leave behind your "old battles"?

    ReplyDelete
  116. Neal Tedford: Margulis is member of the National Academy of Sciences. The same organization you quoted in a post on April 11 to argue your position from authority.

    An appeal to authority is valid when
    * The cited authority has sufficient expertise.
    * The authority is making a statement within their area of expertise.
    * The area of expertise is a valid field of study.
    * There is adequate agreement among authorities in the field.
    * The authority is stating the consensus of those authorities.
    * There is no evidence of undue bias.
    The proper argument against a valid appeal to authority is to the evidence.

    In any case, Margulis is a Darwinist.

    ReplyDelete
  117. Neal Tedford: So, only those members who are under a particular age can be used for your arguments from authority?

    Margulis isn't wrong because she is old. She's wrong on the evidence. As for her fighting old battles, that's quite obvious in her reference to what she was taught (c. 1960).

    Neal Tedford: Yes, there are, as you say, "many exceptions" to the nested hierarchy. Are you ready to embrace the web pattern of life and leave behind your "old battles"?

    The nested hierarchy is strongly supported for eukaryotes. Even for prokaryotes, there is still a discernable phylogeny.

    ReplyDelete
  118. Zachriel said, "In any case, Margulis is a Darwinist. "

    If you mean she is an evolutionists, then yes, I would agree. But, she is quite plain about neo-Darwinism being a failure, so technically I doubt she would like to be lumped into the Darwinist or neo-Darwinist group.

    It is apparent that anyone who disagrees with a neo-Darwinist becomes a target of distain and personal insults.

    It shows the poverty of your theories.

    ReplyDelete
  119. Neal Tedford: But, she is quite plain about neo-Darwinism being a failure, so technically I doubt she would like to be lumped into the Darwinist or neo-Darwinist group.

    Margulis says she is "definitely a Darwinist". That means she accepts the importance of natural selection for determining which variations propagate in nature. However, she is not a neo-Darwinist, meaning she rejects what she considers simplistic and reductionist mutation and selection models. Of course, very few biologists today still adhere to such simplistic models, so it's clear she is still fighting old battles.

    In any case, she considers Intelligent Design to be vacuous, and that evolution is a natural process.

    ReplyDelete
  120. Tedford:

    It shows the poverty of your theories.

    What's your theory, Neal?

    ReplyDelete
  121. Zachriel said, "Of course, very few biologists today still adhere to such simplistic models"

    So she is fighting a make believe strawman that "few" accept anyways?

    So you acknowledge that she is right in what she says is wrong with neo-Darwinian mechanisms, but her problem is that hardly anyone believes in neo-Darwinism anymore?

    Are you trying to have it both ways again?

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  122. This comment has been removed by the author.

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  123. Neal,

    Let me illustrate the difference between Margulis and yourself.

    You have still yet to answer my question, which I'll repeat here for your convenience…

    At a minimum, evolutionary processes played a significant role in speciation.

    Would you agree with this statement or or disagree?


    You've continued to dodge this simple question, dispute the conclusion being based on observations we both appear to agree on.

    You're NOT approaching the issue seriously. Instead, you're simply throwing anything you can find at a theory which you personally find objectionable and hoping it sticks.

    While you might not realize this, or may even attempt to deny it, we can piece this together based on the arguments you present, the observations you accept and your refusal to accept their combined implications. We don't need to guess. You're made this quite obvious.

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  124. Neal,

    On further reflection, the same apparent blindness to our ability to piece together the disingenuous nature of your own objections would also explain your apparent blindness to the significance of evolutionary processes in speciation dispute observations you supposedly accept.

    If you deny or fail to recognize the former, it would come to no surprise that you'd deny or fail to recognize the latter.

    Of course, given the above, you're likely deny or fail to recognize the relevance of this observation as well.

    ReplyDelete
  125. Scott said, "At a minimum, evolutionary processes played a significant role in speciation. "

    Specifically, which evolutionary processes are you referring to and what speciation event that has been observed are you referring to?

    ReplyDelete
  126. Neal,

    1) Is a positive result from a paternity test a reliable indicator of relatedness? Yes, or no.

    ReplyDelete
  127. Derick said, "Is a positive result from a paternity test a reliable indicator of relatedness? Yes, or no. "

    --

    Check with your doctor.

    ReplyDelete
  128. Tedford the Idiot said...

    Derick said, "Is a positive result from a paternity test a reliable indicator of relatedness? Yes, or no. "
    --
    Check with your doctor.


    Wow, look at Tedford the idiot avoid the simple question.

    With fancy footwork like that he should be on Dancing With the Stars.

    ReplyDelete
  129. I asked: "Is a positive result from a paternity test a reliable indicator of relatedness? Yes, or no."

    Neal Tedford: "Check with your doctor."

    Like I said, a pathological aversion to answering simple questions. Neal, would you at least satiate my curiosity and explain why you won't answer this simple question? Do you think it's a trick? Are you not familiar with how a paternity test works? Are you embarrassed by your answer for some odd reason? Does your denomination prohibit you from expressing an opinion on the matter?

    ReplyDelete
  130. Neal, to clarify, a 'yes' or 'no' answer is the minimum response I was asking for. If your answer is "mostly reliable" or "sometimes unreliable", that's fine too. Or, if you think the question isn't valid for some reason or another (grammatically, logically) feel free to express this as well. And feel free to ask me as many yes or no questions as you like. I have nothing to shy away from, as you seem to.

    I really do think it's a simple question, though.

    ReplyDelete
  131. Neal: Specifically, which evolutionary processes are you referring to and what speciation event that has been observed are you referring to?

    I've already clarified this earlier multiple times in multiple threads. Do I need to repeat this here yet again?

    Scott: Over 98% of all species that have ever existed have gone extinct. Is the fact that human beings are part of the less than 2% of species that survived the result of natural, undirected processes or the intentional result of an intelligent designer?

    Neal: The result of an intelligent designer.

    Scott: Would you agree that, at a minimum, random mutations can represent a gradation between neutral and highly detrimental impact on a species, depending on the environment?

    Scott: For example, an mutation could disable the ability to synthesize vitamin-c. In the presence of a food supply that has an ample and acceptable supply of vitamin-c, such a mutation would be neutral. However, in the presence of a food supply that has limited or scarce supply, such a mutation could be mildly or even fatally detrimental.

    Are we both in agreement on this?

    Neal: Scott, okay.

    Scott: If you agree, then it would appear that you'd also agree that, at a minimum, evolutionary processes have had a significant role in the biological complexity we observe. Even if a designer manipulated or compensated for evolutionary processes to ensure the appearance of specific desired features we observe today.


    So, again, are we in agreement on this, at a minimum?

    ReplyDelete
  132. Derick said, "Is a positive result from a paternity test a reliable indicator of relatedness? Yes, or no. "

    Neal: Check with your doctor.

    Neal,

    Do you really think this isn't obvious and transparent? Do you think you're fooling us? If so this is the sort of blindness I'm referring to.

    Or perhaps you know it's obvious, but think this sort of disingenuous response is somehow justified in the case of theories that conflict with your religious beliefs?

    ReplyDelete
  133. Derick, please get to the point and stop being evasive about it and I'll stop being evasive about answering and giving an opinion. Just present your analogy and be done with it. A paternity test is a very precise and measureable test. That's all it is. Using it as some kind of analogy to prove common descent is a rabbit trail.

    ReplyDelete
  134. Scott said, " For example, an mutation could disable the ability to synthesize vitamin-c. In the presence of a food supply that has an ample and acceptable supply of vitamin-c, such a mutation would be neutral. However, in the presence of a food supply that has limited or scarce supply, such a mutation could be mildly or even fatally detrimental"

    ---

    In answer to my question then, you give an example of mutation that disables the ability to synthesize vitamin-c.

    What about the speciation event that was observed? With common descent being supposedly well established you should be able to give many examples of the specific evolutionary processes involved in an observed speciation event. Yes?

    Specific no nonsense examples to these very fair and straightforward questions would be helpful.

    ReplyDelete
  135. Tedford the Idiot said...

    Derick, please get to the point and stop being evasive about it and I'll stop being evasive about answering and giving an opinion. Just present your analogy and be done with it. A paternity test is a very precise and measureable test. That's all it is. Using it as some kind of analogy to prove common descent is a rabbit trail.


    Doing the DNA comparison to establish paternity is a very precise and measurable test.

    Doing the DNA comparison between Sally Hemings' descendants and Thomas Jefferson's DNA is a very precise and measurable test.

    Doing the DNA comparison between Canadian Inuits and Siberians is a very precise and measurable test.

    Doing the DNA comparison between humans and chimps is a very precise and measurable test.

    Why do you accept the first three and reject the fourth?

    A specific no nonsense answer to the very fair and straightforward question would be helpful.

    ReplyDelete
  136. "In answer to my question then, you give an example of mutation that disables the ability to synthesize vitamin-c."

    Molecular basis for the deficiency in humans of gulonolactone oxidase, a key enzyme for ascorbic acid biosynthesis.
    http://www.ncbi.nlm.nih.gov/pubmed/1962571

    "With common descent being supposedly well established you should be able to give many examples of the specific evolutionary processes involved in an observed speciation event. Yes?"

    Yes. Google "speciation gene":

    A Mouse Speciation Gene Encodes a Meiotic Histone H3 Methyltransferase
    www.sciencemag.org/content/323/5912/373

    Evolution: Single-gene speciation by left–right reversal
    www.nature.com/nature/journal/v425/n6959/abs/425679a.html

    Gene Transposition as a Cause of Hybrid Sterility in Drosophila
    http://www.sciencemag.org/content/313/5792/1448.abstract

    And so on....and so on....

    Really Neal, that you don't know something is not a compelling argument against it.

    ReplyDelete
  137. Tedford the Idiot said...

    What about the speciation event that was observed? With common descent being supposedly well established you should be able to give many examples of the specific evolutionary processes involved in an observed speciation event.


    Mechanisms of speciation and observed speciation events

    and a very detailed example

    Speciation through sensory drive in cichlid fish

    ...cue the idiot bellowing "but they're still fish!!!"

    ReplyDelete
  138. RobertC:"Does a .1% minor mystery falsify the other 99.9%?"

    It is not matter of quantity, it is matter of logic. And it is hard to discuss about logic with darwinists.
    "if p then q"

    if common descent then broken genes follow the lineage

    if broken genes do not follow the philogeny darwinist reword the hipotesis.

    "if p then q2"

    if common descent the broken genes follow the lineage unless the broken genes occur in higly probably mutation points.

    How do they differentiate one from another? Looking at the nested hierarchy of traits.

    So traslating to not darwinist wording:

    if common descent the broken genes that follow the nested hierarchy of traits follow the nested hierarchy of traits.

    Remember the planets follow an orbit around the earth only in the little percent that they make epicycles.

    ReplyDelete
  139. Neal Tedford: So she is fighting a make believe strawman that "few" accept anyways?

    The term "neo-Darwinism" is not an exact term. She indicates that she is objecting to what she was taught (c.1960), which is a simplified model of population genetics. The sources of variation are far more complex than naïve notions of mutations. Her work on the endosymbiotic origin of organelles has proved to be largely correct, however, her view that all significant evolution is due to such processes is not supported by the evidence. She still rails against what she was taught half a century ago, while the scientific community has moved on. So yes, she is fighting a strawman.

    Neal Tedford: So you acknowledge that she is right in what she says is wrong with neo-Darwinian mechanisms, but her problem is that hardly anyone believes in neo-Darwinism anymore? Are you trying to have it both ways again?

    Just to repeat, that has to do with equivocation on the term "neo-Darwinism". Margulis uses it to refer to the simplified genetic models of the mid-twentieth century, while others may use it to refer to the modern theory.

    ReplyDelete
  140. Blas: if common descent then broken genes follow the lineage

    Technically, the broken genes are posited to evolve neutrally (this is not always the case), and because genetics are particulate, that means there is a statistical correlation, not an exact one. For instance, a particular site can revert randomly.

    Blas: if broken genes do not follow the philogeny darwinist reword the hipotesis. "if p then q2"

    Not quite. Assuming proper entailment: If p then q, ~q, therefore ~p. The premise has to be modified to be consistent with the result. If p2 then ~q. And should predict a new observation. If p2 then q'.

    It is through this process that a theory changes over time. That's why today's Theory of Evolution today is not yesterday's Theory of Evolution.

    Blas: Remember the planets follow an orbit around the earth only in the little percent that they make epicycles.

    Not sure what that means. Epicycles are usually a small percentage of the overall movement in the geocentric system; there's rarely retrograde.

    By the way, does the Earth follow an elliptical orbit about the Sun?

    ReplyDelete
  141. Neal: "Derick, please get to the point and stop being evasive about it and I'll stop being evasive about answering and giving an opinion. Just present your analogy and be done with it. A paternity test is a very precise and measureable test. That's all it is. Using it as some kind of analogy to prove common descent is a rabbit trail."

    Neal, I've already explained that I have three questions for you. Questions are not analogies. I have no analogy planned based on your responses. Just questions. Clear enough?

    I ask them one at a time, because you can sometimes take months to answer simple, direct questions. There's no point in asking all three if you're going to dance around them as much as you did for the first one. Your apparent terror at stating your views clearly means that I and others usually need to ask you about your opinions in small, easy-to-digest pieces. We have to coax your beliefs out of you. (perhaps you are embarrassed by them. That is perfectly understandable. I would be too.)

    So I take it that in regards to: (1) "Is a positive result from a paternity test a reliable indicator of relatedness?"

    Your answer is:

    Yes; "a paternity test is a very precise and measureable test."

    Good. Next question.

    (2) Are the numerous genetic studies (such as the one by Peter Savolainen et al. and Bridgett vonHoldt et al.) that show that all domestic dogs (canis familiaris) are descended from wolves (canis lupis) reliable? In other words, are tests based on DNA comparison valid when used to compare members within a species?

    ReplyDelete
  142. A more concise way of stating that is:

    (2) If genetic sequencing shows that all dogs are related, is that a reliable indicator of relatedness?

    ReplyDelete
  143. Blas-"if common descent the broken genes follow the lineage unless the broken genes occur in higly probably mutation points."

    Or reversion (only 4 bases!)
    Or mis-sequencing
    Or the last common ancestor had variation at that allele (non-fixed) Some descendent species fix one allele, others fix the other.

    So, I don't think an all-or-nothing scenario, where a small, explainable part of the sample invalidates the rest is justified.

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  144. Zach: “Not quite. Assuming proper entailment: If p then q, ~q, therefore ~p. The premise has to be modified to be consistent with the result. If p2 then ~q. And should predict a new observation. If p2 then q'.”

    Well, I do not see changes in p. Common descent was not modified. And the logic should be:

    if p then q
    as not q, then not p.

    Darwinists changes the expectation, based in nested hierarchy of traits, not expected similarities or differences are called convergence, LGT, vestigial organs, high mutation spots., ocean drifting.
    Then common ancestry is based only in nested hierarchies of traits. That may be good enough, may be common descent is still the best explanation for nested hierarchies of traits. But there is no other overwhelming evidence for common descent.

    “By the way, does the Earth follow an elliptical orbit about the Sun?”

    The data seems to show that, and I am not aware of disagreements in that data.

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  145. RobertC: "Or reversion (only 4 bases!)
    Or mis-sequencing
    Or the last common ancestor had variation at that allele (non-fixed) Some descendent species fix one allele, others fix the other."

    The point is you invoke that mechanisms only when the similarity or difference do not follow philogeny, so you can say that similarities and differences are prove of common descent.
    And I can agree that common descent is not invalidated, and more is still a good explanation for that similarities and differences but do not tell me that they are proves of common descent.

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  146. Blas: Common descent was not modified.

    Sure it has been. Not only has the understanding of the mechanisms improved, but the history of the descent has been revised drastically. In particular, even Darwin didn't propose a perfectly bifurcating tree of descent. He devoted a chapter to hybridization, for instance. Now we know about other crossings, such as endogenous retroviruses (which, forming their own nested hierarchies, help confirm common descent within those branches). With molecular phylogenies, the predicted correlations are statistical in nature.

    Blas: if p then q
    as not q, then not p


    The tilda ~ means "not". If p then q, ~q, therefore ~p.

    Zachriel: By the way, does the Earth follow an elliptical orbit about the Sun?

    Blas: The data seems to show that, and I am not aware of disagreements in that data.

    The Earth's orbit is constantly being perturbed by other bodies, primarily the Moon and Jupiter. Saying the Theory of Gravity predicts an elliptical orbit is a simplification of the actual situation. So pointing out that the Earth does not, in fact, follow an elliptical orbit doesn't falsify the actual Theory of Gravity, only the simplified or strawman version. The Theory of Evolution doesn't posit a perfect nested hierarchy — not even in Darwin's day.

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  147. Blas: The point is you invoke that mechanisms only when the similarity or difference do not follow philogeny, so you can say that similarities and differences are prove of common descent.

    In order to understand why biologists are quite certain of common descent, you have to look at the data. The most important data is the nested hierarchy. Yes, there are exceptions, just like the Earth's orbit is not a perfect ellipse. Any theory has to account for the basic pattern, as well as the exceptions to the pattern.

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  148. RobertC, thanks for the response. Your mouse and Fruit fly examples led to sterility, correct? I do not have access to the whole articles. If so, how does sterility show common descent?

    Your snail example seems like a trivial reproductive isolation event.

    Normally speciation events are said to occur with reproductive isolation. I see examples of this isolation as due to preference or physical size issues. Do you have any research to indicate that after a speciation event, reproduction between the two is completely impossible, even using artifical means? As a follow up, is reproductive isolation ever seen to be temporary ... revert back?

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  149. Neal Tedford: Do you have any research to indicate that after a speciation event, reproduction between the two is completely impossible, even using artifical means?

    Reproductive isolation is often a continuum. Even clearly distinct species can hybridize on occasion. Are you familiar with Darwin's discussion of this in Origin of Species, and why he considered this important evidence in support of his theory?

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  150. I read that fruit flies raise on different foods become reproductively isolated, but this is not due to genetics. It is due to the different pheromones produced by the different bacteria.

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  151. Derick, paternity tests are not equal to genome sequencing comparisons of dogs and wolves.

    But keep in mind that some wolves and dogs can breed, so the idea that dogs came from wolves is possible.

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  152. Neal Tedford said...

    "RobertC, thanks for the response. Your mouse and Fruit fly examples led to sterility, correct? I do not have access to the whole articles. If so, how does sterility show common descent?"

    Sterility between the nascent species-no hybrids. That is, total reproductive isolation. They were one species, now they can't produce offspring or fertile offspring.

    "Your snail example seems like a trivial reproductive isolation event."

    Trivial as in genetically simple? All my examples were intended to be. No Mount Impossible to speciate. The snails are reproductively isolated because of their anatomy. Tell a left-snail trying to mate with a right-snail it is trivial.

    "Normally speciation events are said to occur with reproductive isolation. I see examples of this isolation as due to preference or physical size issues."

    Or genetics. Or other factors. Or isolation followed by genetic events that render them unable to reproduced, even if they tried.

    "Do you have any research to indicate that after a speciation event, reproduction between the two is completely impossible, even using artifical means?"

    Not sure why this matters for studying evolution in nature. I mean, we could genetically engineer a species b mouse expressing a species a sterile transgene and mate a with b (actually I think this was a proof of principle in one paper). But what does this mean for evolution?

    "As a follow up, is reproductive isolation ever seen to be temporary ... revert back?"

    Sure.

    "I read that fruit flies raise on different foods become reproductively isolated, but this is not due to genetics. It is due to the different pheromones produced by the different bacteria."

    Your point? They were reproductively isolated, and without antibiotic treatment, they would have remained that way.

    Neal, I enjoy that you are trying to learn, but I think you're looking for falsifications where there are none.

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  153. RobertC:

    If they were identically genetically, then they were the same spcies by definition. And if they changed diets then they would be able to interbreed.

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  154. Zach: "In order to understand why biologists are quite certain of common descent, you have to look at the data. The most important data is the nested hierarchy. Yes, there are exceptions, just like the Earth's orbit is not a perfect ellipse. Any theory has to account for the basic pattern, as well as the exceptions to the pattern."

    Again you missed the point, you do not call the deviations of the ellipse as prof of gravity, or better (because that deviation are explained by the same theory), you do not call the dark matter a prof of ToG. Do you?
    To explain the exceptions of Common Descent you use new process like LGT, high mutational spots, convergency that are proved by the common descent theory and then you call them prove of common descent.

    Comparing to gravity would be: I found stars moving at speeds do not predicted by ToG, then I explain that by the existance of Dark Matter. Prof of the existance of Dark Matter is the universality of ToG.
    Then Dark Matter proves the ToG.

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  155. Neal, trying to get straight answers out of you is like pulling teeth. I asked:

    (2) If genetic sequencing shows that all dogs are related, is that a reliable indicator of relatedness?

    Neal:Derick, paternity tests are not equal to genome sequencing comparisons of dogs and wolves. But keep in mind that some wolves and dogs can breed, so the idea that dogs came from wolves is possible."

    The idea that dogs are descendants of wolves has always been considered possible. Just like in issues of paternity, it is considered possible that there could exist a parent/child relationship man A and child B, else there would be no reason for the test. The fact that it's possible doesn't mean anything. It's also possible that there isn't a parent/child relationship between man A and child B. That's what a paternity test is for; to determine if there is a parent/child relationship or not. In that same way, genetic tests were carried out on dogs and wolves to determine if there was common ancestry. So the question is: is the positive result from the study a reliable indicator of relatedness between dogs? The question is not: "is it possible that domestic dogs are related," but: "do the genetic studies reliably indicate such."

    Can we reasonably conclude that all dogs are related to each other and to wolves on the basis of these studies?

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  156. natschuster

    I read that fruit flies raise on different foods become reproductively isolated, but this is not due to genetics. It is due to the different pheromones produced by the different bacteria.

    So? I dno't know what specific study you're talking about (it would be helpful if you provided the reference), but if fruit flies become reproductively isolated by non-inheritable or short-term inheritable (epigenetic) causes, I doubt many people would say that is a true speciation event. Maybe it could eventually *lead* to a speciation event, as changes add up independently in the separate linages. The Biological Species Concept (TM) does not have as a big following as introductory biology textbooks make it look like, and I highly doubt anybody would take it as literally to say that non-inheritable isolation is a true speciation (the Biological Species Concept is not the revealed word of Ernst Mayr, it's just an attempt to describe natural phenomena).

    Why do you bring this up?

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  157. Why do you bring this up?

    Sorry, I didn't see the comments on that by others.

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  158. Blas: Again you missed the point, you do not call the deviations of the ellipse as prof of gravity, or better (because that deviation are explained by the same theory), you do not call the dark matter a prof of ToG. Do you?

    In the case of perturbations of the Earth's orbit by the Moon, yes we do. Dark matter is posited to explain the difference between the gravitational effect of visible matter and the apparent gravitational effect of the universe as a whole. In other words, if Theory of Gravity then dark matter. Tests for dark matter include marshalling data from a number of different sources.

    A better example is the anomalous rate of precession of the perihelion of Mercury's orbit. Some thought the anomaly could be explained by another body near the Sun. But this was ruled out. As there was no replacement theory, Newton's Universal Theory of Gravity became Newton's Universal, Except for the Anomalous Rate of Precession of the Perihelion of Mercury's Orbit, Theory of Gravity. Of course, this was eventually explained with a new theory, General Relativity.

    Blas: To explain the exceptions of Common Descent you use new process like LGT, high mutational spots, convergency that are proved by the common descent theory and then you call them prove of common descent.

    They are testable hypotheses.

    Observe the planet Uranus. It follows an elliptical orbit. A closer look reveals an anomaly. Someone proposes that another body is perturbing the orbit. Look and see! Maybe you'll discovery Neptune.

    Blas: Comparing to gravity would be: I found stars moving at speeds do not predicted by ToG, then I explain that by the existance of Dark Matter. Prof of the existance of Dark Matter is the universality of ToG. Then Dark Matter proves the ToG.

    You're close. What you have to do is use *independent* means to test for the existence of the posited dark matter.

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  159. Yes may be we are close, do you have evidence independant from nested hierarchies of traits for convergence, LGT etc..?

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  160. Derrick said, "The question is not: "is it possible that domestic dogs are related," but: "do the genetic studies reliably indicate such."

    I haven't researched how the dna of dogs and wolves are analyzed and compared, so I can't vouch for their accuracy or not. I'm certainly open to it and it sounds reasonable, but I'm not immersed in evolutionary thinking to accept things like this without questions.

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  161. RobertC, can you take your examples one step further then? Zachriel talks about a continuum, but this is where actual evidence begins to give way to speculation.

    It seems like adaptions and variation can occur quite quickly and even revert back quickly, but these are not even necessarily "evolutionary" in the broad meaning of the term.

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  162. Blas: do you have evidence independant from nested hierarchies of traits for {convergence, LGT, vestigial organs, high mutation spots., ocean drifting}.

    There are a number of mechanisms of horizontal gene transfer. Bacterial conjugation was discovered in 1946 by Lederberg & Tatum, for which they won the Nobel Prize in Medicine. A retrovirus inserts itself into a cell's genome by reverse transcription. If this occurs in a germ cell, then it can be passed down to the next generation. Of course, hybridization is a common mechanism. Indeed, the fact that reproductive isolation is often a continuum was considered by Darwin to be important support for his theory of evolution.

    Vestigial structures are directly observed. A simple example is wings on flightless birds. (This doesn't mean they have no function, as many vestigial structures have secondary functions.) Vestigials tend to vary more in their structure as they are under relaxed selection for their primary function.

    Mutational hotspots are also directly observed, as are hypermutators within populations.

    Ocean drifting is directly observed. Large storms can carry organisms for hundreds of miles in very short periods of time. Some organisms, such as coconut trees, have adapted for ocean drifting.

    Darwin was aware of convergence. A simple example is the hydrodynamic shape of fish and dolphins. But as Darwin pointed out, convergence will rarely be so exact that a close look won't reveal the actual ancestry. In this case, dolphins are clearly mammals, not fish.

    To recap, it's important that you see the overall nested hierarchy pattern. When you do, then it will be easier to understand the exceptions.

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  163. Neal: In answer to my question then, you give an example of mutation that disables the ability to synthesize vitamin-c.

    Neal,

    I've clarified the question several times on other threads. I'm simply repeating the question again.

    Scott: If you agree, then it would appear that you'd also agree that, at a minimum, evolutionary processes have had a significant role in the biological complexity we observe. Even if a designer manipulated or compensated for evolutionary processes to ensure the appearance of specific desired features we observe today.

    I'm suggesting that, at a minimum, we can know that evolutionary processes played a significant role in the concrete features of species we observe today. That any species exhibits feature Y today is, in part, the result of it's environment, which includes the existence or non-existence of other species.

    However, I'm specifically referring to the observation that human beings have yet to go extinct. The particular features we exhibit are part of that equation. Yet you claim the fact that human beings have not gone extinct is by design.

    So, you're essentially claiming that intelligent design extends not only to the creation of species but their continued existence today. Of course, this comes as no surprise as the existence of human beings today, and in the near future, plays an important part in your theology.

    Neal: What about the speciation event that was observed? With common descent being supposedly well established you should be able to give many examples of the specific evolutionary processes involved in an observed speciation event. Yes?

    Again, that's not the question I'm asking.

    Take the following hypothetical claims: It was raining yesterday from noon to 5pm in central park, you went jogging yesterday in central park at 2pm and you claim to have remained dry while jogging.

    If we assume these facts are true, in reality, and that all observations should conform to them, we can say that rain had an effect on you while jogging, even if only to be compensated or manipulated by you by using an umbrella, wearing a rain coat, etc. Had you not done so, you would have become wet, which is contrary to the outcome you've claimed. You had to take some form of action to remain dry.

    Right?

    Note that I don't have to observe you running in the rain as we've already agreed that it was raining yesterday in the park where you were jogging. Furthermore, we both agree that going outside while it's raining exposes you water unless you take action to avoid it.

    I don't need to point out exactly which drop cased you to get wet, etc. as this effect is already established and accepted conclusion.

    Following me so far?

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  164. Here's another example.

    You arrive at destination X via car, which you claim was the destination you intended to reach.

    However, each road we travel on has various features that cause vehicles to change direction, such as bumps, different graduations, etc. Rain can cause vehicles to hydroplane. Roads that have yet to be cleared of heavy snow are impassable, which can result in taking a different route.

    Again, if we assume these facts are true, in reality, and that all observations should conform to them, then you would not reach destination X as intended unless you compensated for these factors. They played a role in the outcome.

    Regardless of the exact conditions, it's clear the direction your vehicle takes will be effected by one or more of these road conditions. It's not necessary for me to point out exactly which bump, puddle of water or collection of snowflakes effected the direction of travel. These effects are established and agreed upon by each of us.

    So, again, all I'm doing here is assuming what we already established, along with your claim of design, is true in reality, and that all observations should conform to them.

    To repeat..

    Scott: If you agree, then it would appear that you'd also agree that, at a minimum, evolutionary processes have had a significant role in the biological complexity we observe. Even if a designer manipulated or compensated for evolutionary processes to ensure the appearance of specific desired features we observe today.

    Can we agree on this, at a minimum?

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  165. Neal Tedford: Zachriel talks about a continuum, but this is where actual evidence begins to give way to speculation.

    It's apparent you haven't read Origin of Species. It's dated, but still a classic in terms of presenting a theory and its evidence. In particular, Darwin discusses a number of cases where reproductive isolation is less than complete. And keep in mind, this is not speculation, but observational facts that Darwin marshalled to support his theory.

    This is very standard knowledge in biology: Organisms that are closely related are more likely to produce fertile offspring than those that are distantly related. Brown bears are more likely to produce fertile offspring with other brown bears than with polar bears, and little or no chance with non-bears. Within closely related clusters of organisms, it's possible for only some members to be able to successfully interbreed.

    Some organisms, such as birds and beetles have mechanisms for rapid speciation. Birds use song. Beetles have complex sex organs. Once organisms become reproductively isolated, they will tend to evolve in different directions in order to reduce competitive pressures.

    The key is that there is not always a strict dividing line between varieties and species. This was crucial evidence for Darwin. When you point out that two popualtions may not really be separate species, or that some hominid fossil might be a primitive ape, you are actually reinforcing the idea that there is no strict dividing line. Primitive hominids do look like primitive apes! And varieties often act like separate species, and sometimes separate species will act like varieties! It's a matter of degree.

    -

    "It is certain, on the one hand, that the sterility of various species when crossed is so different in degree and graduates away so insensibly, and, on the other hand, that the fertility of pure species is so easily affected by various circumstances, that for all practical purposes it is most difficult to say where perfect fertility ends and sterility begins. I think no better evidence of this can be required than that the two most experienced observers who have ever lived, namely, Kölreuter and Gärtner, should have arrived at diametrically opposite conclusions in regard to the very same species." — Darwin

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  166. Blas: convergence...

    Forgot to mention, the fact that dolphins clearly group with mammals, but have a hydrodynamic shape like fish, is evidence in support of natural selection.

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  167. Neal: "I haven't researched how the dna of dogs and wolves are analyzed and compared, so I can't vouch for their accuracy or not.

    Here's a start: http://en.wikipedia.org/wiki/Origin_of_the_domestic_dog#DNA_evidence

    You seem to know enough about paternity tests to be able to say with confidence that "a paternity test is a very precise and measureable test." Are you saying that a genetic comparison between humans is 'precise and measurable' but that a genetic comparison between dogs isn't necessarily 'precise and measurable'? Do you think the scientists aren't 'measuring' the difference in DNA? That gene sequencing is 'precise' when applied to human DNA, but not when applied to dog DNA?

    Neal: "I'm certainly open to it and it sounds reasonable, but I'm not immersed in evolutionary thinking to accept things like this without questions."

    Heh. Heh heh heh. Apparently, conducting labor and resource intensive research to answer the question of dog ancestry, then forming an opinion based on the results of the test is "accepting things without question." That's a good one.

    Am I to take it that your answer to:

    2) If genetic sequencing shows that all dogs are related, is that a reliable indicator of relatedness?

    is:

    "not necessarily"?

    Am I understanding your (non)answer? That raises the following questions:

    (2a) [which is more a restatement of (2)] Is it accurate to say that we 'know' that dogs are related, based on the results of these studies?

    (2b) If not genetic tests, how would one determine if all dogs are related? Is that question simply beyond our reach?

    (though I'd rather you give a more direct answer to (2) before addressing (2a) or (2b)

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  168. Tedford the Idiot said...

    Derrick said, "The question is not: "is it possible that domestic dogs are related," but: "do the genetic studies reliably indicate such."

    I haven't researched how the dna of dogs and wolves are analyzed and compared, so I can't vouch for their accuracy or not. I'm certainly open to it and it sounds reasonable, but I'm not immersed in evolutionary thinking to accept things like this without questions.


    You're a lying sack Tedford. You and I covered the genetic evidence for canid evolution in this thread last June.

    When Evidence for Evolution is Actually Evolution of Evidence

    I provided a paper with the latest genetic mapping of the canid genome and the resultant phylogenetic tree right here. I know you saw it because you commented on it.

    What does your Bible teach about bearing false witness Tedford?

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  169. Geoxus:

    I mentioned the fruit fly example because it was sited at one point as an example of reporductive isolation which may eventually lead to a speciation event. But so far, it looks like there has been little or no genetic change, which is what evolution is all about.

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  170. Thorton:

    You're a lying sack Tedford. You and I covered the genetic evidence for canid evolution in this thread last June.

    Good catch. Tedford is a pathological liar, but he's too stupid to keep track of the webs he weaves.

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  171. I haven't been aboe to fined any information about whether the Faroes Island House Mouse mentioned above cannot reproduce with the Common House Mouse. Some people classify it as a subspecies.

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  172. natschuster said...

    I haven't been aboe to fined any information about whether the Faroes Island House Mouse mentioned above cannot reproduce with the Common House Mouse. Some people classify it as a subspecies.


    Non-interfertility has been observed between other mice subspecies as well. For instance, deer mice (Peromyscus maniculatus) and Golden mice (Ochrotomys nuttalli) are not interfertile.

    Artificial insemination
    of deermice (Peromyscus maniculatus) with
    sperm from other rodent species


    So much for there being a single mouse 'kind'.

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  173. natschuster:
    I mentioned the fruit fly example because it was sited at one point as an example of reporductive isolation which may eventually lead to a speciation event.

    Me:
    Maybe it could eventually *lead* to a speciation event, as changes add up independently in the separate linages.

    There is no contradiction.

    But so far, it looks like there has been little or no genetic change, which is what evolution is all about.

    You said it yourself: ...which may eventually lead to a speciation event.

    Again, no contradiction.

    PS: Keep in mind I only know what you have told us about this example.

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  174. Geoxus:

    I konw it doesn't contradict evolution, but it doesn't provide very strong evidence either. That's all.

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  175. Congradulations CH!

    Thanks to your honest research, and other researchers like you, the delusion that is evolution is weakening. More people are seeing the truth. Tennessee and other states are passing legislation to expel the teaching of evolutionary religion in school.

    http://www.cbsnews.com/stories/2011/04/13/scitech/main20053536.shtml

    .

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  176. Scott said, "If you agree, then it would appear that you'd also agree that, at a minimum, evolutionary processes have had a significant role in the biological complexity we observe. Even if a designer manipulated or compensated for evolutionary processes to ensure the appearance of specific desired features we observe today. "



    ---

    Scott, on a lighter note, Abraham Lincoln said, "Every man over forty is responsible for his face."


    Anyway, what specific "evolutionary processes" are you referring too? "Evolutionary processes" is too vague and imprecise for me if this discussion is to go forward. Your asking me to agree to something too vague.

    Are you aware that no one is arguing for fixity of species? No one is arguing that original species have not changed. The debate is about the degree of change. Evolutionists claim spontaneous generation of first life from non-living molecules and then ultimately to mankind via vague evolutionary processes. Empirical studies and actual observation of change shows barriers to increasing biological complexity.

    You said, : "had a significant role in the biological complexity we observe"

    Again, this is vague. Let's cut to the chase. Can you give me a good example of an observed increase in biological specified complexity? Using a software programming example, increasing complexity would not mean deleting, copying, cutting or pasting existing code within the application.

    I'm not sure if you have coded in 1st or 2nd generation programming languages, but even in the higher level languages, increasing the complexity of a program requires coordinated changes in several areas of the code, different sections or modules. A small error or oversight in a change can be fatal to a program.

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  177. Neal Tedford: ... and then ultimately to mankind via vague evolutionary processes.

    Divergence and descent with modification. Natural variations in populations are observed, including observed mechanisms of genetic novelty such as mutation, recombination, gene and genome duplication, with some horizontal mechanisms. Natural selection is observed, and is a direct result of fecundity, heritable variation, and competition for limited resources. Speciation, the process by which populations become reproductively isolated.

    Neal Tedford: Can you give me a good example of an observed increase in biological specified complexity?

    A gene duplication followed by functional migration would seem to qualify, but to answer your claim, you would have to provide an unambiguous measure of "bSC".

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  178. Zachriel said, "The key is that there is not always a strict dividing line between varieties and species. This was crucial evidence for Darwin."

    --

    The species definition problem segways into the conflict with evolutionists about whether or not a true speciation event has ever been observed.

    Also, the Cambrian Explosion and other periods of abrupt appearance of distinct life forms, continues to plague the evolutionary storyline.

    And then there's this gem... you said, "Primitive hominids do look like primitive apes!"

    ---

    They look like apes, because they were apes!


    You know, if something quacks like a duck and looks like a duck...

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  179. Neal Tedford: The species definition problem segways into the conflict with evolutionists about whether or not a true speciation event has ever been observed.

    Sometimes populations can become reproductively isolated in a single event, such as polyploidy. But much of the time it is a slower event. Populations become isolated, and then diverge.

    Neal Tedford: Also, the Cambrian Explosion and other periods of abrupt appearance of distinct life forms, continues to plague the evolutionary storyline.

    There is a great deal now known about the Cambrian Explosion. There were predecessors long before the period. There was a rapid diversification, but well within known rates of evolution.

    Neal Tedford: And then there's this gem... you said, "Primitive hominids do look like primitive apes!" They look like apes, because they were apes!

    It's almost as if you really don't bother to read what others write.

    Humans are apes, so that's not the question. Rather, because organisms typically evolve over long periods of time, the close you get to the common ancestor, the harder it is to distinguish the two lines. That's the expected pattern! The previous, creationist, line of thoguht, is that species were inviolate because they were separately created. But that is not the case. Even in extant nature, it can be hard to determine the difference betweeen species and varieties. Again, this is the pattern we expect from an evolutionary process.

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  180. Zach: “There are a number of mechanisms of horizontal gene transfer. Bacterial conjugation was discovered in 1946 by Lederberg & Tatum, for which they won the Nobel Prize in Medicine. A retrovirus inserts itself into a cell's genome by reverse transcription. If this occurs in a germ cell, then it can be passed down to the next generation. Of course, hybridization is a common mechanism. Indeed, the fact that reproductive isolation is often a continuum was considered by Darwin to be important support for his theory of evolution”
    As you can see here: http://download.cell.com/current-biology/pdf/PIIS0960982211001011.pdf?intermediate=true or here http://www.pnas.org/content/105/44/17023.full.
    Evolutionist says: “this similar sequences should be of common origin, as they do not have a common ancestor according to philogeny (nested hierarchy of traits) the should be LGT”
    So that are not evidences of LGT independant of nested hierarchy. I bet the “mutational hotspots”
    also are deducted from violation of the nested hierachy in the same way.

    Zach: “Ocean drifting is directly observed. Large storms can carry organisms for hundreds of miles in very short periods of time. Some organisms, such as coconut trees, have adapted for ocean drifting”.

    Sure?, storms can make mammals cross the ocean from africa to madagascar? The common ancestor of southamerican monkeys crossed the atlantic? Any prove of that other than the “nested hierarchy of traits”?
    Zach: “Darwin was aware of convergence. A simple example is the hydrodynamic shape of fish and dolphins. But as Darwin pointed out, convergence will rarely be so exact that a close look won't reveal the actual ancestry. In this case, dolphins are clearly mammals, not fish.”

    Again you are demostrating convergence based on the nested hierachy of traits. There is no independant evidence.

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  181. Zachriel said, " Natural variations in populations are observed, including observed mechanisms of genetic novelty such as mutation, recombination, gene and genome duplication, with some horizontal mechanisms. Natural selection is observed, and is a direct result of fecundity, heritable variation, and competition for limited resources. Speciation, the process by which populations become reproductively isolated. "

    Sounds close to neo-Darwinism to me. What in your mind is the difference?

    Okay, so give me a specific real life example of an observed "gene duplication followed by functional migration would seem to qualify" event.

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  182. Neal:Anyway, what specific "evolutionary processes" are you referring too? "Evolutionary processes" is too vague and imprecise for me if this discussion is to go forward. Your asking me to agree to something too vague.

    I'm referring to the process we've already agreed upon and established, at a minimum.

    Neal: Are you aware that no one is arguing for fixity of species?

    Neal,

    Are you aware of the minimal impactions of what you've already accepted? I'm only assuming that what already established, along with your own claim of design, are true in reality and that all observations should conform to them. I've given two examples of this process in illustrate this in detail.

    Again we've already established or accept the following.…

    01. At a minimum. random mutations can represent a gradation between neutral and highly detrimental impact on a species, depending on the environment.

    Note that, for the sake of argument, I'm not assuming that random mutations can provide beneficial features. Instead, I'm only assuming mutations are either neutral or cause some degree of detriment. The fitness of a species remains neutral or degrades. Neutral mutations are under no negative selective pressure.

    02. The fossil record indicates species have come and gone. Over 98% of all species that have ever existed have gone extinct.

    03. It's clear that the environment changes over time. This includes changes as part of [02]

    Furthermore, you claim..

    04. The fact that human beings are part of the less than 2% of species that survived is the intentional result of an intelligent designer, rather than the result of natural, undirected processes. The specific appearance of human beings in essentially the same form we take today, along with our continued existence, is an intentional outcome chosen by an intelligent designer.

    So, again, if we assume [01-03] along with your claim of [04] is true, in realty, and that all observations should conform to [01-04], then it would seem that, at minimum, random mutations and natural selection [neutral or negative] has played a significant roll in the biological complexity we observe. Even if a designer manipulated or compensated for evolutionary processes to ensure the appearance of specific desired features we observe today.

    At a minimum, this is all I'm asking you to accept.

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  183. Neal,

    2) If genetic sequencing shows that all dogs are related, is that a reliable indicator of relatedness? In other words, is it accurate to say that we 'know' that all dogs are related to each other, based on the results of these studies?

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  185. Blas: So that are not evidences of LGT independant of nested hierarchy.

    Huh? We have direct observations confirming horizontal gene transfer, such as bacterial conjugation, retroviruse and hybridization, as well as mutational hotspots and ocean drifting. Is there some reason you copied the text, but didn't read it?

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  187. Peter said...

    Congradulations CH!

    Thanks to your honest research, and other researchers like you, the delusion that is evolution is weakening. More people are seeing the truth. Tennessee and other states are passing legislation to expel the teaching of evolutionary religion in school.

    http://www.cbsnews.com/stories/2011/04/13/scitech/main20053536.shtml

    ==============================

    here's an interesting little quote from the article.

    But the ideas proposed as alternatives to evolution -- creationism and intelligent design-- are not science. Creationism is religion. Intelligent design is just plain sneaky: It is rooted in religion but couched in pseudoscience with enough scientific-sounding mumbo-jumbo to confuse a kid into thinking there just might be something to it.

    This guy is obviously biased.

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  188. Neal Tedford: Sounds close to neo-Darwinism to me. What in your mind is the difference?

    Neo-Darwinism has several related meanings. It can refer to the modern Theory of Evolution, or it can refer to the original synthesis of Mendelian genetics with Darwinism from the middle of the twentieth-century. Originally, it referred to non-Larmarckian evolution.

    Margulis is using it to refer to the early period of the modern synthesis whereby it was thought that mutation, recombination and selection were sufficient to explain all diversity. Mutation is much too simple a concept to explain the diversity of mechanisms involved in biological novelty.

    Neal Tedford: Okay, so give me a specific real life example of an observed "gene duplication followed by functional migration would seem to qualify" event.

    We can't know if an event qualifies because you haven't provided an unambiguous metric of "bSC".

    In any case, 6-Aminohexanoate-dimer hydrolase recently evolved by duplication and mutation of an existing gene.

    Negoro et al., X-ray Crystallographic Analysis of 6-Aminohexanoate-Dimer Hydrolase, Journal of Biological Chemistry 2005.

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  189. Derick, genome sequencing has come a long way in the last decade, but it is still a relatively new field. The genome has multiple levels of complexity that we just do not understand yet.

    The dog sequencing is probably right on but I do not have any confidence in evolutionary biologists interpret anything correctly where even an ounce of speculation is required. I have about as much confidence in evolutionists to correctly interpret anything as I would with geocentrists plotting a space trip for me.

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  191. Zachriel said, "Margulis is using it to refer to the early period of the modern synthesis whereby it was thought that mutation, recombination and selection were sufficient to explain all diversity. "

    What would you add to the list then?

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  192. Scott, if a computer virus or a weekend hacker messed with a computer OS, does that explain the specified complexity of the OS? Did the virus or weekend hacker have a significant role in the complexity of the computer OS?

    You said, "Furthermore, you claim..

    04. The fact that human beings are part of the less than 2% of species that survived is the intentional result of an intelligent designer, rather than the result of natural, undirected processes. "


    ---

    I did not say any such thing.

    Whose intention was it that passenger pigeons be hunted to extinction?

    Your saying things I did not say, your questions are vague and out in left field.

    What's the price of tea in china today?

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  193. Zachriel, no frame shift mutation according to:

    Negoro S, Ohki T, Shibata N, et al. (June 2007). "Nylon-oligomer degrading enzyme/substrate complex: catalytic mechanism of 6-aminohexanoate-dimer hydrolase". J. Mol. Biol. 370 (1): 142–56. doi:10.1016/j.jmb.2007.04.043. PMID 17512009.

    Got another one?

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  194. Zachriel: Margulis is using it to refer to the early period of the modern synthesis whereby it was thought that mutation, recombination and selection were sufficient to explain all diversity.

    Neal Tedford: What would you add to the list then?

    Well, you could start with the endosymbiotic origin of organelles, neutral theory, gene and genome duplication, canalization, and a variety of horizontal mechanisms, among others.

    Neal Tedford: no frame shift mutation according to {Negora et al. 2007).

    No, it's due to mutation. You asked for a gene duplication followed by divergence. Does this process represent an increase in bSC ("biological Specified Complexity")?

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  195. Neal: Neal: Whose intention was it that passenger pigeons be hunted to extinction?

    For human beings to avoid being hunted to extinction, we must be capable of defending ourselves against other predators. The deck must be stacked in our favor. We can say the same about natural disasters. Statistically speaking, we're just about due for another catastrophic meteor strike that could cause mass extinctions on a global scale due to drastic changes in the environment.

    In other words, we must maintain this advantage, over time, in varying environmental conditions, or we'll go extinct. Furthermore, you seem to agree that it's possible for neutral mutations occur, which would allow them to become fixed in a population. At some point in the future, these neutral mutations can become fatal when conditions change.

    Perhaps you think a designer manipulated the environment to ensure neutral mutations in human beings remained neural, rather than detrimental?

    Perhaps you think a designer augmented neutral mutations with beneficial mutations to counter act their effects?

    Perhaps you think a designer stopped neutral mutations from occurring or reversed them when conditions changed which would have caused them to be detrimental?

    Even if you assume one or all of the above is true, at minimum, random mutations and natural selection [neutral or negative] has played a significant roll in the biological complexity we observe. Even if a designer manipulated or compensated for evolutionary processes to ensure the appearance of specific desired features we observe today.

    Can we agree on this, at a minimum?

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  196. -- reposting --

    Neal: Scott, if a computer virus or a weekend hacker messed with a computer OS, does that explain the specified complexity of the OS? Did the virus or weekend hacker have a significant role in the complexity of the computer OS?

    Neal,

    Apparently, you're either not reading my comments. Again…

    Note that, for the sake of argument, I'm not assuming that random mutations can provide beneficial features. Instead, I'm only assuming mutations are either neutral or cause some degree of detriment. The fitness of a species remains neutral or degrades. Neutral mutations are under no negative selective pressure.

    Is there something about this you do not understand?


    Neal: Whose intention was it that passenger pigeons be hunted to extinction?

    Again, apparently you're not reading my comments.

    then it would seem that, at minimum, random mutations and natural selection [neutral or negative] has played a significant roll in the biological complexity we observe.

    This doesn't necessitate that all extinctions were caused by evolutionary processes. Playing a significant role is not the same as being the exclusive cause.

    Why are you being so evasive?

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  197. -- reposting --

    Neal: I did not say any such thing.

    You agreed to it here…

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  198. Ambiorix said:

    "But the ideas proposed as alternatives to evolution -- creationism and intelligent design-- are not science. Creationism is religion. Intelligent design is just plain sneaky: It is rooted in religion but couched in pseudoscience with enough scientific-sounding mumbo-jumbo to confuse a kid into thinking there just might be something to it."

    On the contrary, evolution is not science. It is fiction - an atheistic delusion. True, Creationism isn't science. But it is true nevertheless because God created life. Evolution is false. The claims of evolution are beyond the capabilities of science. Science can not explain how life starts because life is too complex and arises in explosions, not gradual steps. Intelligent design is science because it describes reality, unlike evolution. It is evolution that was deceiving the public at large. But now, thanks to the great work of CH and others like him society is not being taken in by the evolutionary charlatans.

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  199. Scott, your questions are often hard to follow. In the previous post I was simply agreeing that humans were intelligently designed. If you understood that to mean more than that, then I apologize for being unclear... but to clarify, all I really meant to agreed to was that humans were intelligently designed. I don't have a clue as to how your point about the 2% extinction stuff is relevant.

    I take your question about biological complexity to mean an INCREASE in biological specified complexity. Zachriel tried to answer that with an example (I sense an upcoming post from him about the various meanings of "mutation" and such). Perhaps you would like to try an example too.

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  200. Peter:

    On the contrary, evolution is not science. It is fiction - an atheistic delusion.

    Really? An atheistic delusion shared by nearly all theistic scientists. And you came to this conclusion how exactly? Could it be years of studying the evidence in the scientific literature? Or could it be that you are another lazy creationist that is too afraid to look into the evidence for evolution, and prefers to accept the lies published at creationist websites? I'm guessing option #2. Please correct me if I'm wrong.

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