Tuesday, August 07, 2012

Note to David Klinghoffer, When You find Yourself in a Hole, Stop Digging

Some of you might recall the recent Chromosome 2 kerfuffle. It started when Carl Zimmer asked David Klinghoffer a simple question. Zimmer asked him to describe the evidence to support his claim that the fusion site didn't look like it should if two primitive ape chromosomes had fused to produce human chromosome 2.

Rather than simply answer the question, the IDiots circled the wagons then went into attack mode. Eventually, after a lot of pressure, they got around to answering the question; apparently there is no evidence to support their claim [And Finally the Hounding Duck Can Rest].

Of course by then they were so deep in their hole that the sun don't shine.

The IDiots are at it again. Paul McBride criticized their attack on junk DNA by pointing out that IDiots distort history in order to make scientists look stupid. Specifically, they say that when scientists discovered that only a few percent of our genome encoded protein they claimed that all the rest of the DNA was junk. In other words, scientists claimed that all noncoding DNA was junk.

I've also blogged extensively about this false claim, especially in Jonathan Wells' book The Myth of Junk DNA [Watch Jonathan Wells Screw Up].

A few days ago I praised Jonathan McLatchie for finally admitting that what the IDiots said was false [Intelligent Design Creationists Attempt to (re)Define Junk DNA]. McLatchie said, "As stated above, no credible scientist claims that all non-coding DNA is 'junk.'" This is about as close to admitting error as the IDiots ever get.

I suggested that Jonathan McLatchie should talk to Jonathan Wells and set him straight on the history of biochemistry and molecular biology.

Enter David Klinghoffer, a creationist with no scientific background whatsoever [On Junk DNA, Where's the Contradiction?]. Getting out his shovel, he writes,
Larry Moran thinks he's caught Discovery Institute's Jonathan Wells and ENV's Jonathan M. in an embarrassing contradiction. The topic: "junk DNA." Moran crows:
Oops! Jonathan Wells says that some biologists referred to all noncoding DNA as junk but McLatchie admits that this is not true.

Those two need to have a talk. It's what honest people do.
You know where this is headed, don't you?

The IDiots must defend their icon, Jonathan Wells, and if that means tossing Jonathan McLatchis to the wolves, so be it. Remember that McLatchie had the honesty to admit, "... no credible scientist claims that all non-coding DNA is 'junk.'

Here's David Klinghoffer ...
Jonathan Wells and Jonathan M. express themselves in different terms but there's no significant disagreement that any honest reader can detect. As Wells documents in his book The Myth of Junk DNA, some well known biologists have pretty flatly equated non-protein-coding DNA with junk. Richard Dawkins is one -- in 1976 and again in 2009. U.C. Berkeley's John Avise is another (2010). Others, like Kenneth Miller (1994), imply such an equation. Jerry Coyne (2009) sets up a dichotomy between those genes that "function" by coding for proteins and those that don't function and therefore are to be dismissed as "pseudogenes." Just as evolutionary theory predicts, writes Coyne, "Our genome -- and that of other species -- are truly well populated graveyards of dead genes."
We seem to have a bit of a problem here. I'm certain that David Klinghoffer would like to think of Richard Dawkins, John Avise, Ken Miller, and Jerry Coyne as "credible scientists" otherwise why bother attacking them?

Jonathan McLatchie probably thinks they are credible scientists as well. I've read lots of books and articles by these credible scientist and I can assure you that none of them think that all noncoding DNA is junk. McLatchie is correct.

But what about Jonathan Wells. What "different terms" does he use to make his views compatible with more honest Intellignet Design Creatinists like Jonathan McLatchie? Let's look at pages 15 and 19 of The Myth of Junk DNA.
In the 1950s, neo-Dawrinists equated genes with DNA sequences and assumed that their biological significance lay in the proteins they encoded. But when molecular biologists discovered in the 1970s that most of our DNA does not code for proteins, neo-Darwinists called noncoding DNA "junk" and attributed it to molecular accidents that have accumulated in the course of evolution.

...

Yet by 1970 biologists already knew that much of our DNA does not encode proteins. Although some suggested that non-protein-coding DNA might help regulate the production of proteins from DNA templates, the dominant view was that non-protein-coding regions had no function.
Here's my challenge to Jonathan McLatchie; do you think Wells is correct? Do you think that in the 1970s there were significant numbers of credible scientists who thought that all noncoding DNA was junk?

UPDATE: Paul McBride has responded to McLatchie pointing out that McLatchie misrepresents Casey Luskin: Jonathan M gives a qualitative response on junk DNA.


18 comments :

  1. The quote from Jonathan Wells on p. 19 of "Myth of Junk DNA" was quoted at me by Jonathan M in order to prove the exact opposite of what Wells actually said.

    Wells said, in the quote above, that most molecular biologists equated non-coding DNA = junk DNA.

    Jonathan M quoted that very quote at me, in order to prove the opposite, that Wells did not say that molecular biologists equated non-coding DNA = junk DNA. This is absurd and dishonest, but Jonathan M closed comments at ENV before I could call him out on his dishonesty.

    Wells said: "Yet by 1970 biologists already knew that much of our DNA does not encode proteins. Although some suggested that non-protein-coding DNA might help to regulate the production of proteins from DNA templates, the dominant view was that non-protein-coding regions had no function." [Wells, "Myth of Junk DNA", chapter 2, p.19]

    In fact Jonathan M's citation proved that I was right, but ENV closed all comments so that I could not expose lying Jonathan M and Jonathan Wells. See my comments here at ENV, where I kick Luskin's lying ass:

    [See: Luskin at ENV says scientists said Non-coding DNA = Junk.]

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  2. Here is Casey Luskin lying about scientists, claiming that molecular biologists equated non-coding DNA = Junk. This was directed at me in a brief exchange at ENV before the lying cowards closed comments because I was kicking their asses.

    Luskin vs. Diogenes: "Contra your [Diogenes'] claims, many of these scientists essentially equated noncoding DNA with junk. As Jonathan Wells documents...

    [Luskin then lists many quote mines from Wells' book, in which Luskin and Wells insert ellipses and remove phrases and clauses to deceive non-scientist readers]

    Luskin vs. Diogenes: Many additional examples could be given. It's very convenient for some scientists to argue, in 2012, that the genome isn't full of useless junk. Good for them... But that doesn't change the fact that for decades, evolutionary scientists presumed that non-coding DNA was largely junk. Your [Diogenes'] comment is attempting to rewrite history...

    If you post the entire quote of a quote you only partly quoted, it shows that many biologists equated non-coding DNA with "junk" DNA....

    So there you have it. According to Nature, non-coding DNA “used to be called ‘junk’ DNA”, but we now know that many of these noncoding elements have regulatory functions…”" [Luskin at ENV]

    (Luskin above was citing Erika Check Hayden, a journalist in a News & Views article in Nature (March 2010), not a molecular biologist. She did not say that non-coding DNA used to be called junk DNA; that was Luskin's invention.)

    Luskin: "In fact, the junk-DNA mindset, which was born and bred from the Darwinian paradigm, even stifled research... The journal Science reported that the junk DNA mindset "repelled mainstream researchers from studying non-coding DNA." [Luskin at ENV]

    (Here Luskin was misrepresenting Wojciech Makalowski (2003), another "Perspective" type article, which said no such thing.)

    Luskin: But I [Casey Luskin] am claiming that for years, Darwinian scientists claimed that non-coding DNA was largely junk, and that we’ve discovered massive amounts of function for non-coding DNA, and that the trendline is strongly in favor of function...

    Luskin: there are literally hundreds [of papers] out there finding vast levels of functionality for non-coding DNA. [Luskin at ENV]

    Luskin: "In 2003, Scientific American reported that one type of non-coding DNA called introns 'were immediately assumed to be evolutionary junk.'"... [Luskin at ENV]

    So Casey Luskin is on record lying about scientists, saying that they equated non-coding DNA = junk DNA. We caught them. They can try to walk it back but we got those lying weasels.

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  3. Here is creationist Russell W. Carlson, positively reviewing Wells' book.

    Carlson insists that the main message of Wells' book is that molecular biologists equated non-coding DNA = junk DNA.

    Russell W. Carlson: "In The Myth of Junk DNA Jonathan Wells tells the intriguing story of `junk' DNA-the idea that non-protein coding DNA, which accounts for the majority of the DNA in the genome, is non-functional and without purpose... In recent years, however, numerous researchers... have discovered many functions for non-protein coding DNA, which are thoroughly reviewed by Wells in this book. Unfortunately, in their effort to keep the `junk' label attached to non-protein coding DNA so that it remains in the box of Darwinian evolution, a number of prominent Darwinists continue to insist...that it is largely left-over waste from the evolutionary process. ...Wells's book not only informs its readers of very recent research results, but also encourages them to think objectively and clearly about a key discovery in biology...It is a great read."

    This is the take home message from Wells' book, and this quote was approvingly cited by ID creationists as an accurate description of Wells' book "The Myth of Junk DNA."

    So Wells was lying outright when he said molecular biologists equated non-coding DNA = junk DNA.

    Now ID creationists were caught lying, they want to re-write history about it.

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  4. Here is a video of Jonathan Wells, caught live, lying through his teeth about how molecular biologists equated non-coding DNA = junk DNA. Now we have caught the lying sack of crap lying through his teeth, the creationist want to rewrite history and deny that they ever said what they said. But we have Wells live on video lying through his teeth.

    Watch Wells lie about what scientists said:

    [At 4:46] “In the 1960’s and 1970’s, however, molecular biologists discovered that most human DNA does not code for proteins. Since the Central Dogma is that "DNA makes RNA makes protein makes us," non-protein-coding DNA appeared to many biologists to be "junk."

    (This is false about non-coding DNA and it is also false about defining the Central Dogma of molecular biology, as Larry pointed out already.)

    [At 11:45] "In fact, about 98% of our genome is not protein coding, and this is what gave rise to the notion of junk DNA... this does not mean that that DNA [non-coding] is junk."

    Slide: “Evidence that non-protein-coding DNA is functional (most common slide in talk, appearing many times)

    [At 22:35] Slide: “Conclusion: There are still parts of non-protein-coding DNA for which no function is known. Yet new functions are constantly being discovered, so any argument for Darwinian evolution that rests on “junk DNA” (as Francis Collins’ does) must constantly retreat in the face of new evidence.

    Now lying creationist Jonathan M wants to re-write history and pretend that was never said.

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  5. Here is our own commenter Atheistoclast, aka Joe Borzergmehr, lying through his teeth about how scientists equated non-coding DNA = junk DNA.

    Here is what Atheistoclast said this week:

    Atheistoclast this week: "Wells has never ever claimed that the scientists of the 1970s believed every single nucleotide of ncDNA to be junk"

    (We have many quotes of lying Jonathan Wells saying exactly that.)

    Here is Atheistoclast a week ago, saying that molecular biologists equated non-coding DNA = junk DNA.

    Atheistoclast: "The search for more and more functional ncDNA, previously regarded as being junk, is now a major part of finding cures for genetic diseases." [Atheistoclast just last week]

    Now lying weasel Atheistoclast is trying to walk that back!

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    Replies
    1. You could at least spell my surname correctly.

      You are making a spurious argument. In the 1970s, virtually all ncDNA seemed to have no function. Scientists did not know about long ncRNA genes, and were not aware of the amount of cis-regulatory elements other than those found within promoters. Hence, 99% of ncDNA was indeed regarded as being "junk".

      Like I say, mutations in ncDNA - previously regarded as being "junk" - have been found to play a role in disease. I suggest you read this paper on the subject:

      http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001074

      Why are so obsessed with quibbling over 1%?

      Delete
    2. Atheistoclast: Why are so obsessed with quibbling over 1%?

      The creationist charge is entirely about a fraction of a fraction of a percent.

      If 10 bp of a 1000-bp pseudogene are found (by evolutionists, natch) to function as a regulatory element, ID creationists use that as an argument for why ID creationists should control science labs and universities.

      10 bp out of 3 billion bp in the human genome is 0.0000003%. That is less than a millionth of a percent.

      And yet, when evolutionist scientists discover a new function in less than a millionth of a percent of the genome, ID creationists use that as a reason to demand that the control of science labs should be taken away from the evolutionist scientists who made those discoveries, and power and authority over laboratories should be given to ID creationist thumbsuckers, like lawyer Casey Luskin, lawyer Barry Arrington, Klinghoffer of the unknown occupation, etc.

      Here is Evolution News and Views demanding that control of science labs be taken away from the scientists who made the discoveries, and handed over to creationist thumbsuckers.

      Evolution News and Views: "Recently Darwinians made the same kind of mistake with their myth of 'junk DNA'... One wonders how much further along science would be today if ID scientists had the power to direct research about "vestigial organs" and "junk DNA" instead of letting the Darwin power structure tell everyone, "there's nothing to see here." One wonders, further, how much pain and suffering might have been avoided.” -- [Evolution News & Views, July 20, 2012.]

      They say: people will suffer-- children will die-- unless we take the power over science labs away from the evolutionist scientists who discovered those functions in less than one percent of the genome, and give the power to thumbsucking ID creationists like lawyer Casey Luskin and Klingleberry of the unknown occupation, and lying Jonathan Wells, who made no discoveries at all.

      Jonathan Wells: “Coyne and Avise are professors of genetics at major universities, so they cannot claim ignorance of the genomic evidence without thereby admitting negligence or incompetence... Like Dawkins, Shermer and Kitcher, they have forfeited any claim they might have had to be speaking for science. [Jonathan Wells, The Myth of Junk DNA, pp. 97-98]

      Real geneticists like Coyne and Avise have "forfeited" their claim to "speak for science" because they might have been wrong about a fraction of a fraction of a percent (and even this is not clear), thus the right to "speak for science" should be handed over to lying creationist Jonathan Wells, who never made any discoveries in genetics, never found any new functions in non-coding DNA, said cancer is not caused by genetic mutations, and said HIV does not cause AIDS.

      Your entire "Myth of Junk DNA" is based on a fraction of a fraction of a fraction of a fraction of one percent.

      I apologize for misspelling your name, but if you use an anonymous ID I'm not sure you have much to complain about, Joseph Esfandiar Hannon Bozorgmehr.

      Delete
    3. I must also repeat this quote from Atheistoclast himself:

      Atheistoclast: “Science is not easy. It is hard stuff. Those who put their hands up in the air and give up trying to find difficult answers to vexing problems, and who make unwarranted assertions, have no place within science. [Atheistoclast just last week]

      Above Atheistoclast said that real geneticists like Larry Moran (and many others) "have no place within science" because Atheistoclast has evidence they were wrong about a fraction of a percent of the genome.

      That fraction of a percent, about which they were allegedly wrong (and there isn't really evidence of that) is enough for Atheistoclast to demand that many real geneticists, including Larry Moran, and molecular biologists, should be booted out of their labs. To make room for... whom, exactly?

      It is exactly that fraction of a percent that is the basis of your demand for real geneticists like Larry to be fired. But now you say we shouldn't quibble about 1%?

      Delete
  6. Why did creationists like Jonathan Wells, Casey Luskin, ENV, Jonathan Maclatchie, and Atheistoclast lie about Junk DNA?

    Because they wanted power. ID creationists lied to make scientists look stupid-- by smearing scientists, dragging them down, ID creationists could make themselves looks smarter by comparison.

    Obviously ID creationists don't do real research or make real discoveries, so their only hope for getting power and authority is to make scientists look stupid. And to do that, ID creationists lie about what scientists teach and how they do research.

    Here's how they use their lies do demand power and authority for ID creationists.

    In this post at ENV, the ID creationists imply that sick patients have suffered (perhaps died) because evolutionists do science and control science labs-- that evolutionists kill people. But, they say, if ID creationists had the power to control science labs, those people would not have died.

    Evolution News and Views: "A favorite criticism of ID is that it is a science stopper. The opposite is true... Evolutionary theory, in fact, has been worse than a science stopper: its predictions have been flat out wrong. ... Recently Darwinians made the same kind of mistake with their myth of "junk DNA" (see David Klinghoffer's take on that persistent myth).

    ...Intelligent design, in contrast, offers a host of promising questions for research. One wonders how much further along science would be today if ID scientists had the power to direct research about "vestigial organs" and "junk DNA" instead of letting the Darwin power structure tell everyone, "there's nothing to see here." One wonders, further, how much pain and suffering might have been avoided.”
    -- [Evolution News & Views July 20, 2012.]

    Note that all novel functions found in non-coding DNA in the last 50 years have been found by evolutionists, and not even so much as 10 base pairs of non-coding DNA have had a novel function discovered by creationists or ID proponents (out of 3 billion bp in the human genome.)

    But, the lying creationists say, if non-scientist thumbsuckers like lawyer Casey Luskin or lawyer Barry Arrington or lawyer Phillip Johnson controlled the science labs, they would be making the discoveries, curing the diseases and saving lives. Right.

    They say: give the power over science labs to these creationist thumbsucking lawyers-- or else kids will die.

    Jonathan Wells: “Coyne and Avise are professors of genetics at major universities, so they cannot claim ignorance of the genomic evidence without thereby admitting negligence or incompetence... Like Dawkins, Shermer and Kitcher, they have forfeited any claim they might have had to be speaking for science. [Jonathan Wells, The Myth of Junk DNA, pp. 97-98]

    Wells accused molecular biologists of equating non-coding DNA = Junk DNA. Wells was lying. But, he cannot lose authority to "speak for science" because he never had any before. He can only speak for superstitious witch doctors.

    Casey Luskin: "In fact, the junk-DNA mindset, which was born and bred from the Darwinian paradigm, even stifled research... The journal Science reported that the junk DNA mindset "repelled mainstream researchers from studying non-coding DNA." [Luskin at ENV]

    Atheistoclast: “Science is not easy. It is hard stuff. Those who put their hands up in the air and give up trying to find difficult answers to vexing problems, and who make unwarranted assertions, have no place within science. [Atheistoclast just last week]

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  7. So many ID propagandist lies documented in this thread it's ridiculous.

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  8. I do not see anywhere, in the quote block recounting Jonathan Wells' comments from pages 15 and 19 of his book, The Myth of Junk DNA, a claim that "all" scientists in a particular camp think that non-coding DNA is junk, nor a claim that a significant number of scientists in a particular camp think that "all" non-coding DNA is junk.

    The portion you quoted from Wells is clearly a summary view of what was taking place in a broad field with lots of participants. When reading passages that appear to be summaries, intelligent, flexible readers only infer an absolute claim if the language is distinctly absolute. If words like "all" and "every" do not appear, we take it as a possibility that some may have disagreed, and that there was probably some variation within the position. Summary discussions have that character; they gloss over detail in order to give a broad picture, thus saving time.

    Unless you can provide me with a quotation from Wells insisting explicitly that the positions of neo-Darwinists were absolute, or stating explicitly that "every" scientist believed a certain thing, I have to disagree with you. There is no apparent disagreement between Wells and McLatchy.

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    1. (Mmm, Diogenes smell fresh creatio-snacks. Dat some tasty Creationizm!)

      A sophist shows up to argue that ID creationists like Wells are not lying because, actually, their writing had no information content. That's the creationist defense: we weren't lying because our sentences contained no information.

      Philwynk: I do not see anywhere, in the quote block recounting Jonathan Wells' comments... a claim that a significant number of scientists in a particular camp think that "all" non-coding DNA is junk.

      Uh, d'ya think maybe it was here?

      Jonathan Wells: ..the dominant view was that non-protein-coding regions had no function.

      What do you think "dominant view" means, sophist? Maybe you should tell us what "dominant view" means, sophist.

      Even if by "dominant view" Wells meant just 10% of molecular biologists, or even only one molecular biologist, Jonathan Wells would still be a liar, because Wells has no evidence that even one, not even one molecular biologist ever equated non-coding DNA = junk DNA. If you now redefine "dominant view" as meaning one molecular biologist, Wells would still be a lying sack of crap.

      Perhaps you think you are not a liar because Wells said "dominant view" but you said "a significant number." Tell us mathematically, is "a significant number" more or less than "the dominant view"? If they are different, can you mathematically quantify... oh never mind. To the extent that your sentences contain information, they are lies.

      Philwynk: I do not see anywhere, in the quote block recounting Jonathan Wells' comments...a claim that "all" scientists in a particular camp think that non-coding DNA is junk

      Jonathan Wells wrote: ...in the 1970s...neo-Darwinists called noncoding DNA "junk"...

      Ah, since creationist liars now seek to use sophistry to redefine the plain meaning of their own writing, can you please tell me what is the NEW meaning of Jonathan Wells' sentences NOW?

      When he writes, "neo-Darwinists called noncoding DNA 'junk'", is the new meaning "a majority"? 90%? 51%? "A minority"? One percent of all scientists? One scientist? Even by all of these NEW definitions, Jonathan Wells is a liar.

      In fact, Jonathan Wells has no evidence of any "neo-Darwinist" scientist ever calling non-coding DNA "junk", not even one, not then and not now.

      PhilWank: If words like "all" and "every" do not appear, we take it as a possibility that some may have disagreed

      It is not that "some may have disagreed", you sophist, it is that no molecular biologists ever agreed. Not even one agreed. Your lying creationist Jonathan Wells has no evidence that even one molecular biologist equated non-coding DNA = junk.

      Moreover, all molecular biologists had to know, in order to do their work, in laboratory experiments, that things like regulatory elements and RNA genes exist, are functional and are non-coding. Or they would be expelled from grad school in their second year. Every single molecular biologist had to know it or he'd get expelled.

      Philwynk: Unless you can provide me with a quotation from Wells...stating explicitly that "every" scientist believed a certain thing, I have to disagree with you

      Oh, so the only kind of lies that disturb sociopaths are lies that contain the word "every"? News flash: it is possible for some people to lie without using the word "every."

      Liars like Jonathan Wells and Casey Luskin don't have any evidence that any molecular biologists ever equated non-coding DNA = junk DNA. If you have any evidence that any molecular biologists ever equated non-coding DNA = junk DNA, then present a quote from a molecular biologist equating them, right here right now, or admit your trusted authorities are liars.

      Delete
    2. philwynk that's nothing short of historical revisionism you're engaging in here. Then again, I guess you guys are already so used to making a piece of text fit whatever proposition you need to be true in the moment this is simply to be expected.

      Delete
  9. I'm shocked, shocked, to find lying going on at ENV.

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  10. If anyone is digging a hole, its you Larry Moran.

    It is clear as day that those scientists you cite believe most of our genome is junk. It is incredibly disingenuous to claim that since these same scientist did not claim that 'all' non-coding DNA was junk, that ID cannot assert these scientists are calling non-coding DNA junk.

    Any sensible person would simply reply to Mr. Moran, WTF?

    Like Johnathan M. alludes to in his most recent post, your pedantry says it all about you. You are not interested in honest representation of what IDers say, you are simply interested in smearing ID, cuz well that's all you got.

    How 'Moranic' can you get? Guess only a 'Moran' could tell you.

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    1. Steve, Even wikipedia gets it right, but DI cannot.

      http://en.wikipedia.org/wiki/Noncoding_DNA
      "In genetics, noncoding DNA describes components of an organism's DNA sequences that do not encode for protein sequences."

      And

      "Much of this DNA has no known biological function and is sometimes referred to as "junk DNA". However, many types of noncoding DNA sequences do have known biological functions, including the transcriptional and translational regulation of protein-coding sequences."

      and

      [Noncoding functional RNA's] "are functional RNA molecules that are not translated into protein. Examples of noncoding RNA include ribosomal RNA, transfer RNA, Piwi-interacting RNA and microRNA."

      NO ONE considers tRNA, rRNA, promoters, etc junk DNA. Therefore no one says ALL non-coding DNA is junk.

      If we said all ID proponents were Christian, young earth creationists, would you point out the error?

      Delete
  11. Give it up Diogenes,

    Your verbosity is no substitute for an argument.

    Your shreiks of "LIES!" is telling.

    what's that old saying, "Who cries the loudest is the guilty one.

    You claim lies precisely because you are no stranger to lying.

    A little honesty, please!!!

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  12. Steve: "You claim lies precisely because you are no stranger to lying."

    If there were evidence that I wrote anything inaccurate, you would have presented that evidence. You did not present any evidence because you can't show any inaccuracies in what I wrote.

    Steve: "what's that old saying, "Who cries the loudest is the guilty one."

    You use three exclamation points in a row. So, you're crying the loudest.

    All I did was copy-n-paste the actual words written by ID proponents. Their own words indict them as liars. Their own words burn them.

    In fact, this post has been up several days and no ID defender has posted any evidence nor any quotes from ID advocates that defend their obviously false statements.

    You can say whatever you like, but you can't present evidence to dispute that all major ID proponents, including Casey Luskin and Jonathan Wells, are pathological liars. They're your trusted authorities. You trust them.

    ReplyDelete