Home » Humor, Intelligent Design, theistic evolution » “[The Discovery Institute] needs to be destroyed”

“[The Discovery Institute] needs to be destroyed”

After Darwinist Steve Matheson debated Stephen Meyer at Biola, various essays appeared on the internet pointing out Matheson’s numerous errors and oversights. In the face of having his assertions publicly discredited (see a summary in Fact Free Science of Matheson), he wrote an open letter to Stephen Meyer.

Your Discovery Institute is a horrific mistake, an epic intellectual tragedy that is degrading the minds of those who consume its products and bringing dishonor to you and to the church. It is for good reason that Casey Luskin is held in such extreme contempt by your movement’s critics, and there’s something truly sick about the pattern of attacks that your operatives launched in the weeks after the Biola event. It’s clear that you have a cadre of attack dogs that do this work for you…I can’t state this strongly enough: the Discovery Institute is a dangerous cancer on the Christian intellect, both because of its unyielding commitment to dishonesty and because of its creepy mission…It needs to be destroyed, and I will do what I can to bring that about.

Steve Matheson,
Open Letter to Stephen Meyer

Even though Matheson really said those words, I felt that this blog posting is most appropriately filed under the Humor category. :-)

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81 Responses to “[The Discovery Institute] needs to be destroyed”

  1. Casey Luskin is an awesome guy, Matheson shouldn’t be dissing him.

  2. By the way, notice the use of the Skull and Crossbone when Matheson says here

    I think it will be useful to send a clear message to the Discovery Institute as an organization, now that I’ve seen its mode of response to me since Meyer and I met. Here’s my simple message:

    Skull and Crossbone

  3. “Bow”? … not “Bones”, Sal?

  4. 4
    William J. Murray

    That anyone, let alone a distinguished member of the scientific and academic community, would deliberately spew such frothing hate for all the public to see is tragic.

    I think Matheson is taking this debate far, far too personally.

  5. “Your Discovery Institute is a horrific mistake, an epic intellectual tragedy that is degrading the minds of those who consume its products and bringing dishonor to you and to the church”.

    So I guess as far as he’s concerned, this is an ecclesiastical problem? He acknowledges that he can’t provide a sufficient materialistic explanation for information’s origin and he calls someone else who does provide such an explanation as dishonoring the church. Who is confused here and who is making this a theological issue?

    Debates offer opportunities for rebuttal on both sides. Matheson needs some thicker skin or offer up a better argument. The noise increases when the logic breaks down.
    Fairly typical of a materialist, so far as I can tell.

  6. I’m still trying to digest this. What means, exactly, is Matheson prepared to use in the destruction of Discovery? Does Discovery have the right to exist ueberhaupt? Does freedom of thought and expression apply to Discovery?

  7. Charlie:

    “Bow”? … not “Bones”, Sal?

    Thank you. I corrected my comments. Thank you again!!!

  8. The problem most TE’s have with ID is that the information ID brings to the table is that of a “Tinkering” designer (who most think is God) and one that could not get it right the first time but has to come back to correct His mistakes. To many of them ID is demeaning the omniscient, omnipotent God.

    The problem is that this point of view claims to know the mind of God and how He would work. And it is not ID’s part to say the designer is God but to be honest the way religion is quoted here, most of the pro ID people believe it is the Christian God.

  9. toc:

    Fairly typical of a materialist, so far as I can tell.

    My understanding is that Matheson considers himself a Christian and teaches at a religious institution. (I could be wrong, so anyone weigh in if I’m mis-stating his position).

    His website has a banner which features a Chrsitian cross (though not distintly one), and higher up on the banner is also a photo of Darwin.

    If Matheson is a TE, he echoes sympathies similar to many other TE’s: “the Discovery Institute is a dangerous cancer on the Christian intellect”.

  10. Setting aside the question of ID and evolution, where Matheson argument was discredited was with respect to the functionality of introns.

    One of the authors of the paper in the prestigious scientific journal Nature Barash that strongly support Sternberg and Meyer’s claims, did research on the links between disease and malformed introns.

    If introns are indeed vital to physical health, quite apart from the ID debate, it’s really bad form for Matheson to be dissing investigation into the question of intron functionality. SERIOUSLY bad form!

    Frankly he ought to be grateful that Sternberg and Wells have pointed out his mistakes.

  11. Quite apart for the ID/Evolution debate, Matheson is insisting introns have little or no function, and worse, he labels defenders of intron functionality as drinker’s of kool-aide (a reference to poison kool-aide of Jim Jones). But what if Matheson is wrong. Why not rather encourage exporation even into a daring hypothesis such as intron functionality. It could have extremely important implications for medical advancement. Matheson belligerence is possibly making him party to “the biggest mistake in the history of molecular biology”.

    It would seem to me, on those grounds alone, quite apart from the issue of ID and Evolution, that the Discovery Institute, on the issue of junk DNA, is clearly on the right side of the betterment of the human condition and medical science.

    Matheson’s determination to destroy the Discovery Institute seems more of a personal vendetta, not rooted in a commitment to scientific exploration.

    I’d like to express my thanks to the Discovery Institute staff for all that they’ve done toward the advancement of the human condition and their work in promoting the awareness of important issues.

    To that end, I just now sent a donation (which I should have done long ago). UD readers who feel the Discovery Institute has done a good public service and who wish to make a donation (especially to their Center for Science and Culture) can do so here:

    http://www.discovery.org/csc/donate.php

    Uncommon Descent also accepts donations to help pay for our administrative costs. There is a button on the UD webpage through which donations can be made.

    It is apparent there are forces that would rather serve personal vendettas than advance the cause of scientific exploration. Readers are invited to help the cause of intellectual freedom.

    Thanks in advance to all who are willing to help in whatever capacity they are able.

    PS
    As a matter of public disclosure, I personally make no money for my involvement in Intelligent Design.

  12. Scordova Re. post 9 -

    Sorry, I meant “materialist” in the sense of methodological materialism or naturalism, rather like Ayala, Collins, et al and quite distinct from Philosophical Naturalism.

  13. Steve Matheson said:

    //there’s something truly sick about the pattern of attacks that your operatives launched in the weeks after the Biola event. It’s clear that you have a cadre of attack dogs that do this work for you, and some of them seem unconstrained by standards of integrity//

    Whilst I don’t agree with Matheson’s viscious, vitriolic, exaggerated and nasty tone here, I think there is a grain of truth in what he is saying. After Biola, the ID blogs did not seem courteous to Steve Matheson, but instead seemed to be championing a victory. For example, there was a post with the headline: “Which Steve said ‘design is an excellent and irrefutable explanation’?” – where upon reading seeing the context, it was clear that Matheson did not say this as a concession to ID. Aside from posts with a misleading title, I think posts with a “winner-loser” feel like these tend to shut down dialogue. Maybe such a format is necessary with ultra-Darwinists like PZ Myers et al. but they don’t seem necessary with more respectful critics like Matheson used to be. Indeed, as evidenced by Matheson’s recent nasty turn, “winner-loser” posts seem only to antagonise such people and make them even more hostile to ID. If we want more debates and interaction with these type of people, then it might be worth writing about their arguments in a less hostile and more ‘dialogue-esque’ way.

  14. Green,

    I would agree with you, save for the fact that Matheson largely behaved this way far in advance of this event. It wasn’t like he was critical but considerate, showed up at Biola thinking he was the loyal opposition among friends, and then suddenly turned hostile in response to the fallout. Go read his review of Meyer’s book. Go read his review of Behe’s book. There was no “recent nasty turn” because Matheson has been nasty for a long time.

    And worst of all? The criticism he got from the DI, and Sternberg in particular, was honestly rather tame – especially compared to Matheson himself. The guy clearly is one of those “can dish it out but can’t take it” sorts.

    That said, I agree entirely that ID needs to engage respectful critics – and respectful critics should be treated with respect in turn. But it’s a two-way street.

  15. Matheson claims “attack dogs” and “operatives” launched a pattern of attacks:

    For the UD reader’s benefit here are some of the essays written after the Biola event:

    Which Steve Said Design

    and

    Gotcha on Checking Stephen Meyer

    and

    Mathesons Intron Fairy Tale

    and

    Let’s Do the Math Again

    All these were posted after the event, with the last one one June 3 before Matheson wrote his letter on June 6.

    And Jonathan Wells wrote more on June 8:
    The Fact Free Science of Matheson

    Anika Smith reported Doug Axe’s contributions on June 10:

    Doug Axe Knows His Work

    I invite the readers to decide for themselves if these postings at ENV are deserving of the responses offered by Matheson.

  16. scordova,

    Arguments for the utility of intron transcripts will eventually have to deal with the fact that megabases of the genome can be deleted with no obvious ill effect, as in the well known experiments on mice. If the Discovery Institute would like to pursue that line of experimentation, it could directly prove how much of the mouse genome was necessary. I think pursuing such an experimental program would increase the respect people have for the DI across the spectrum of the ID debate.

  17. Is Matheson free to post on UD’s website?

  18. 18

    Not that it matters much, but the guy calling for the “destruction” of his intellectual enemies – who is backed by the virtual whole of the academy, the whole of the media, and the public policy and legal machine of the science establishment – is whining about “attack dogs” out to get him.

    Frankly, I never thought much about Matheson the few times his name has perculated to the surface. But now going back and reading his words. Wow.

    He is bloated with certainty.

    He may need to go spend a few days at a children’s burn unit and get his head straight.

    pfft

  19. 19

    One thing I have learned from my debates with evolutionists, they HATE free speech.

    This was also proven by the censorship of the California Science Center which has since decided to settle the lawsuit brought against them by the Discovery Institute.

  20. Nakashima wrote:

    Arguments for the utility of intron transcripts will eventually have to deal with the fact that megabases of the genome can be deleted with no obvious ill effect

    That’s an obviously flawed Darwinist viewpoint. Robust systems can suffer massive deletions and still function. Knockout experiments are a clumsy way to adjudicate function.

    See an example of how such reasoning actually failed in biological analysis:

    Airplane Magnetos Contingency Designs and Reasons ID will Prevail

    Briefly, we can knock out huge amounts of computational power in 4 of the 5 navigations systems of the Space Shuttle, and the shuttle can still get back to Earth.

    If we applied “knock out” standard to space shuttles, you’d easily conclude all the spare and contingency systems of the shuttle were useless!

    I provided a citation where such reasoning resulted in mis-analysis of a biolgical system.

    The fact that biological systems can self-heal is good evidence we can knock systems out and there is little if any detectable effect along various dimensions of functionality.

  21. Further, in my other thread on Matheson, I pointed out how you might well be able to knock something out and there is no ill effect in the majority of context, but there could be ill effect in another context. It may well be in such contexts, the functional importance is elucidated.

    You could probably knockout entire modules of Windows 7 (like say ceratin printer drivers) and see contexts where there is absolutely no ill effect, maybe even improvement. It would be illigitimate however to say such modules are non-functional.

    Finally, though I appreciate you raising this important issue, this thread about “destroying the DI” is not the place for this discussion.

    There is another thread on that topic.

  22. An open letter to Steve Matheson:

    Dear Steve Matheson,

    I have read your open letter about the Discovery Institute and I am sorry that you feel that way.

    Perhaps you should take a step back and ask yourself “why are these people attacking me?”

    Could it be due the diatribe you have been spewing about Intelligent Design in general and more specifically about Stephen C Meyer and his book “The Signature in the Cell”?

    The point being is that your words and actions have consequences and these alleged attacks- is correcting your mistakes and educating you really attacking you?- are your karma for your spewage.

    The lesson learned should be next time you attack someone make sure that you have your facts straight or it will come back at you from all angles.

    If you can’t take it then don’t dish it out.

    Your buddy,

    Joe G

    PS for the record I think Darwinism, neo-Darwinism and materialism in general are horrific mistakes- epic intellectual tragedies that has degraded the minds of all who have consumed it, making dishonor a badge proudly displayed.

  23. Steve Matheson posted here briefly in July 2008 and writes about his experience on his blog at that time. He made some negative comments and was banned. I do not know if he has been back since. He made a big point of how this place was a cesspool so I doubt he would want to post here.

  24. I can’t state this strongly enough: the Discovery Institute is a dangerous cancer on the Christian intellect, both because of its unyielding commitment to dishonesty and because of its creepy mission…It needs to be destroyed, and I will do what I can to bring that about.

    Steve Matheson is a certifiable kook, who is obviously suffering from the double mental illness of delusions of grandeur enhanced by irrational, paranoid conspiracy theories.

    His essay makes this conclusion obvious. He should seek professional help immediately, before this pathology mutates into something more serious.

  25. Jerry @23: As I recall, Matheson didn’t fare very well here. Among other things, he appeared to be personally offended simply because he was being asked to respond to rigorous intellectual challenges. Indeed, he continually characterized those challenges as personal attacks even though they were nothing of the kind. For the most part, he didn’t even bother offering counter arguments. Eventually, he just withdrew. Getting banned was the best thing that could have happened to him since it provided him an opportunity to change his status from defeated warrior to oppressed victim.

    Following that, he established two or three special websites recounting his side of the dialogue and leaving out all the comments from the other side. It’s easy to look good when your adversary is not allowed to speak.

  26. Here is a howler by Matheson:

    Meyer’s statement is ludicrous. The human genome contains at least 190,000 introns (though it’s been recently estimated to contain almost 210,000). Together those introns comprise almost 1/4 of the human genome. One fourth. That’s 768 million base pairs. And biologists have identified “important functional roles” for a handful of them. How many? Oh, probably a dozen, but let’s be really generous. Let’s say that a hundred introns in the human genome are known to have “important functional roles.” Oh fine, let’s make it a thousand. Well, guys, that leaves at least 189,000 introns without function,

    To understand why this is a howler, consider that the space shuttle has probably many systems whose functions would not be recognizable to matheson. Does lack of knowledge of those systems make these systems non functional. Of course not. But by Mathesonian logic, if we only know the function of a handful of parts, the rest must be non functional. If you don’t believe that such Mathesonian logic exists, then re-read the statement by Matheson:

    Let’s say that a hundred introns in the human genome are known to have “important functional roles.” Oh fine, let’s make it a thousand. Well, guys, that leaves at least 189,000 introns without function,

    So according to Matheson, if we know the roles of 1000 introns, then the other 189,000 have no function. HOWLER!

    Did it ever occur to Matheson the functions could exist independent of whether we recognize them or not?

    Unfortunately, Matheson is making serious presumption that could hamper medical science. What if introns are vital to health? By his standard, if we don’t know an intron has function, it must not have one. BAD BAD SCIENCE!!!!

    Perhaps he was unware introns implication in various diseases such as this one:

    An LKB1 AT-AC intron mutation causes Peutz-Jeghers syndrome via splicing at noncanonical cryptic splice sites

    or how about the one listed in Wiki:

    a point mutation in intron 7 of the human gene TPH1 is highly correlated to the development of the psychiatric disorder schizophrenia.[6]

    That’s two, do you think we could actually make it to 12?

    How about the disease identified in A deep intronic mutation in the RB1 gene leads to intronic sequence exonisation

    That’s err, 3. Can I make it to 12?

    I’ll let Bergmann list 9 more:

    http://www.rae.org/introns.html

    At least a dozen studies shave found evidence that introns are either directly or indirectly involved in cancer causation. Examples include evidence that introns are involved in transcriptional regulation of apoprotein B, E, and A-1145 and that introns may be involved in regulating neoplasm developments.46

    Cytolytic T lymphocyte clones used to study melanomas found the gene coding for the antigen recognized by the cytolytic T lymphocyte was the same gene which codes for N-acetylglucosaminyl-transferase V. The antigenic peptide recognized by the cytolytic T lymphocyte was found to be encoded by a sequence located inside an intron. The researchers found that the mRNA containing the introns coding for the antigen was not found at significant levels in nominal tissues but was observed to be present in close to half the melanoma tissues studied. The researchers concluded that a promoter located near the end of the relevant intron was activated in melanoma cells, resulting in the production of an mRNA that codes for the antigen.47

    Defective glutathione S-transferase and N-acetyl-transferase enzymes have been associated with an increased risk of developing both lung and bladder cancer. The research results are inconsistent, though, and several studies have failed to find associations. According to some studies, the lung cancer risk is elevated up to 40-fold in subpopulations that contain both the high-risk cytochrome P-450 type Al and glutathione S-transferase Ml genotypes which are a result of mutations in introns or other silent areas of DNA. One study on the glutathione S-transferase M3 gene found a mutant three-base deletion in intron 6 of the wild type glutathione S-transferase allele.48 This defect may be related to neoplasm development, but exactly how is unknown.

    Megonigal, et al. used panhandle PCR to clone MLL genomic breakpoints in two pediatric treatment-related leukemias.49 The panhandle PCR identified a fusion of MLL intron 6 with a previously uncharacterized sequence in MLL intron 1 which the researchers concluded was consistent with a partial duplication. The breakpoints in both cases were located in Alu repeats, suggesting that the Alu sequences were an important contributor to the rearrangements they found

    I’ve listed a 12 cases where introns are believe to serve an important role.

    Matheson obviously didn’t do his homework, and if he did, he wasn’t sharing citations like the ones I just provided.

    But there are 190,000 of these introns! Is matheson so sure we’ll never find more important roles for introns in all these 190,000 the more we study it?

    Oh, I get it, in Matheson’s mind, if we’re not aware of a function, it doesn’t exist. Good one Matheson. By that standard of reasoning, we should not look for hereditary diseases due to intron issues, since introns by your definition don’t serve useful functions.

    So much for putting ideology and saving face ahead of caring for the human medical condition.

    Like I said. HOWLER!

  27. Casey Luskin in 2007 reported an exchange with our friend Dr. Andras Pelloiniz in IS Pandas Thumb Suppressing Truth about Junk DNA?

    In that report, Dr. Pellionisz observed:

    The Scientist, and elaborated in more detail in my “Obituary of Junk DNA “http://www.junkdna.com/#obituary_of_junk_dna” uncounted millions of people died miserable deaths while scientists were looking for the “gene” causing their illnesses – and were not even supposed to look anywhere but under the lamp illuminating only 1.3% of the genome (the genes).

    One person with a Junk DNA disease ” http://www.junkdna.com/junkdna_diseases.html ” is my dear friend and fellow-pioneer of Junk DNA scientific research; Dr. Malcolm J. Simons, the Honorary Chairman of IPGS “http://www.junkdna.com/ipgs_staged/founders.html”

    As documented in the full transcript of the video Genius of Junk “http://www.abc.net.au/catalyst/stories/s898887.htm” award-winning science documentary (never aired in the USA, guess why), Malcolm, as a Darwinist voiced in the 2003 filming his 1987 conviction against the “Junk Frame” this way:

    Under Darwinistic notions you would think that junk would drop off under the theory of natural selection just like species drop off if they hit ecological niches which is incompatible with survival. If they can adapt to those niches, then those that can survive and those that can’t die. There’s the notion. If you apply that to the DNA sequence, then the coding region genes which survived have a function and by the way the non coding sequences have survived as well. So the proposition would have to be that if they’re there, they’ve got a function [MJS]

    How do you think his fellow-Darwinist scientists received his assertion (1987) that “Junk DNA” had a function?

    When I showed the professional geneticists the data, which indicated to me that the 95% non-coding region wasn’t junk, and was ordered…The reaction was smiling disbelief at best – you’re off your friggin’ head and if you’re any good at squash – stick to your day job [MJS]

    PS
    As a side note, the above exchange evidences how Darwinism can be variously interpreted in favor or against the notion of Junk DNA.

    The point however, is that it is unwise to presume, like Matheson does, that because we haven’t elucidated function, it must not exist.

  28. From :

    Talking Trash

    Steve Matheson:

    creationist claims that non-coding DNA is largely functional are ludicrous

    Are you sure you want to stick to that story Steve? :-)

    Can you cite the scientific methodology that determines something has no function? Ignorance of function doesn’t count as a methodology.

    Furthermore, as noted above, Knockout Experiments can be a dubious methodology. Out of context observations (particualrly for context dependent functions) aren’t good methodologies. But for sure, not perceiving a function (at this stage of our collective research) is definitely not a good methodology for arguing something has no function. If that attitude were adopted we wouldn’t have bothered to discover intron related diseases. Thankfully there are some researchers that don’t adopt the Mathesonian method of assessing the existence of function.

  29. “It needs to be destroyed, and I will do what I can to bring that about.”

    Hey, this seems quite similar to what a very disappointed Caiafas sings in the movie “J.C. Superstar”:

    “Fools! You have no perception! The stakes we are gambling are terribly high. We must crush him completely! So like John before him, this Jesus must die!”

  30. oops in the real citation
    “frighteningly”
    is used instead of “terribly”.

    “Fools! You have no perception! The stakes we are gambling are frighteningly high. We must crush him completely! So like John before him, this Jesus must die!”

  31. scordova,

    I’ve listed a 12 cases where introns are believe to serve an important role.

    No, you’ve listed 12 cases where changing the intron caused disease, mainly by causing a protein to be created that was not created previously (ie changing the intron into an exon). That reinforces how important proteins are, not how important mRNA transcripts are. You have demonstrated anything about the normal intron itself. If you wanted to do that, you could try knocking it out…

  32. Clive,

    [StephenB:] It’s easy to look good when your adversary is not allowed to speak.

    StephenB seems to agree with me.

    I still have no response from you.

  33. This is in response to recent posts by toc and Sal Cordova on Professor Steve Matheson’s current religious beliefs.

    The following three comments are on Professor Steve Matheson’s Web page, in response to his Open Letter to Stephen Meyer . Readers might find them of interest.

    *********************************

    COMMENT #1 by Human Ape (1 week ago)

    About Stephen Matheson
    Associate Professor of Biology, Calvin College, Grand Rapids, Michigan
    Reformed Christian
    Developmental cell biologist
    Evolutionist

    Stephen Matheson, your letter to the creationist Stephen Meyer is priceless. I especially like your desire to destroy the Discovery Institute (“It needs to be destroyed, and I will do what I can to bring that about.”)

    Now the only thing you need to do to become a perfect person is throw out your Christian death cult. Certainly you must agree it’s pointless to believe in a magic god fairy who never had anything to do. And it’s even worse to believe in the worthless dead preacher man Jeebus.

    You already sound like an atheist. You share the moral values of atheists. Now you just need to become an atheist.

    *********************************

    COMMENT #2 by Kevin DeGraaf (1 week ago, in reply to Human Ape)

    Like “Human Ape”, I take issue with the supernaturalist elements in the otherwise excellent open letter. I keenly await Prof. Matheson’s response to Ape’s comment, as someone who has unsuccessfully attempted to engage Prof. Matheson on this very point.

    *********************************

    COMMENT #3 by SteveMatheson (1 week ago in reply to Kevin DeGraaf)

    Hi Kevin and Ape,

    Yeah, I’m a believer. Right now, that applies about 5 days a week. The other two I’m a skeptic. Kevin, I’m sorry that you object to the “supernaturalist elements” of my letter, though I don’t know where they are. As for “engaging” me on faith, let’s hear a question. I make no guarantees about your satisfaction with my answers. Ape, thanks for the compliment. My very best friends right now are both atheists, and I am honored to be compared to them.

    *********************************

    MY COMMENT:

    This is very sad. Notwithstanding our vigorous disagreements with Professor Matheson on the subject of intelligent design, I think the first thing we should do is pray that he doesn’t lose his faith in God and in Christianity.

    If there’s a moral to this story, it’s that we tend to become like the people we hang out with.

  34. Vj,

    Thanks for the info.

    Personally I respect Atheist, though I disagree. There might be reasonable arguments in favor of not believing in God, but Darwinism isn’t one of them.

    Sal

  35. “Personally I respect Atheist, though I disagree. There might be reasonable arguments in favor of not believing in God, but Darwinism isn’t one of them.”

    If there are, I’ve never heard them.

  36. Scordova-

    As far as I can tell atheism has no sond argument in support of it. The biggest one is the problem of suffering which was refuted centuries ago by Leibniz and I just so happened to watch Tim Keller’s talk at Google where he mentions that the problem of suffering hasn’t been viewed as a tenablr argument since 1982. This is basically for the same reasons that Leibniz used to refute and that is that God allows some evil for a greater good, that humans may or may not ever be able to understand. William Lane Craig takes a different tact and shows that the existence of evil is not incompatible with the existence of God. Also, if there is truly evil in tue world then there has to be a go otherwise how can we recognize evil.

    Dawkins’ approach is to say that the existence of God is unlikely, but that is because he does not acknowledge the basic evidence for God the most basic of which is that God ids a necessary being and also Antony Flew’s recognition of the teleological argument is in sark contrast to Dawkins’ assertion of illisory desiflgn or teleology.

    Hitchens wants to make the argument that religious people have done many bad things which is obviously a fallacious argument not to mention horribly simplistic.

  37. Here are a few more examples of introns implicated in function:

    Alzheimer’s disease due to an intronic presenilin-1 (PSEN1 intron 4) mutation

    and

    Tay-Sachs disease: Intron 7 splice junction mutation in two Portuguese patients

    and

    Alternative splicing in intron 13 of the human eNOS gene: a potential mechanism for regulating eNOS activity

    and

    Nucleotide Mutation Friedrich Ataxia

    and

    Evidence for a calcium regulated, bidirectional intronic promoter in the murine TCR V1 gene

    Including those listed, that’s more than 12 introns implicated with function. Does Matheson have problems counting above 12. He said, 12 would be generous, but as I’ve demonstrated, and could demonstrate further, his claim that “12 is generous” is indefensible.

    Oh, I get it, according to Mathesonian logic, if he doesn’t believe something has function, it doesn’t have function.

    Thankfully there are medical researchers that don’t subscribe to Mathesonian logic.

  38. Oops i think Hitchens is an anti-theist in that he thinks that if there is a god He’s not all that great. He uses the prenise i mentioned though which is still obviously fallacious.

  39. To quote Pellionisz above:

    uncounted millions of people died miserable deaths while scientists were looking for the “gene” causing their illnesses – and were not even supposed to look anywhere but under the lamp illuminating only 1.3% of the genome (the genes)

    Pellionisz is expressing the fact that if there are hereditary diseases existing in the 98.7% of the human genome we call junk, then we’re looking in the wrong places!!!!!!!

    If so, Matheson and Moran are party to this hindrance of medical advancement.

    PS
    An indirectly related article to this issue, but it hints of the problem:

    A Decade Later, Genetic Map Yields Few New Cures

    Well if you’re ignoring the possiblity hereditary diseases are in the 98.7% of the genome which many view as junk, then maybe that’s the reason we’re not finding more hereditary diseases linked to the genome!!!!!!!!!!!!!!!!!!!!!!

    SHEESH!

  40. 40

    Toronto,

    Clive,

    [StephenB:] It’s easy to look good when your adversary is not allowed to speak.

    StephenB seems to agree with me.

    I still have no response from you.

    I agree too. Did you have a point?

  41. Clive Hayden @ 40,

    If you agree with StephenB and myself, take all the anti-ID people who have shown they are civil, off moderation.

    This gives everyone, both pro-ID and anti-ID equal opportunity to respond to each other.

    I have many times seen a comment directed at me that had a lot of effort put into it by a pro-ID person but I can’t put that degree of effort into a reply, since it may pop up in the middle of the thread where no one sees it.

    Recent comments also don’t indicate that my reply has cleared moderation so nobody is going to look for it.

    If you truly believe in a free exchange of ideas, put us on an equal footing.

  42. @Jerry

    -”The problem most TE’s have with ID is that the information ID brings to the table is that of a “Tinkering” designer (who most think is God) and one that could not get it right the first time but has to come back to correct His mistakes. To many of them ID is demeaning the omniscient, omnipotent God”

    The notion of “tinkering” is rather troublesome in my opinion. A better way to phrase it would be in terms of God’s participation in reality through constant sustenance and creation.

  43. –vjtorley: “If there’s a moral to this story, it’s that we tend to become like the people we hang out with.”

    I agree. I further submit the following:

    Christians who attempt to reconcile a purposeful Christianity with a purposeless Darwinism always end up giving Darwin the last word.

  44. 44

    I’m going to invite Steve over to discuss some things here very soon. Who knows if he’ll actually engage with the folks here, but it’s worth a shot.

  45. Scordova-

    As far as I can tell atheism has no sond argument in support of it.

    First off, I was echoing what a respected ID proponent, Lee Spetner said in his book Not By Chance

    “There may be good reasons for being an atheist, but the neo-Darwinian theory of evolution isn’t one of them.”

    Lee Spetner
    [Page 174]

    When I say “reasonable arguments”, not that I’m saying that it is necessarily correct, but it may be a reasonable inference by a person where he is in his life’s journey at the time.

    I’m of the opinion faith in God does not come through our power to reason but by His gracious revealation in people’s lives.

    I will leave it to each person to follow his conscience. But I think before someone decides to become an Atheist because of Darwinism (Provine calls Darwinism: “The Greatest Engine of Atheism”), we should consider if the theory is correct.

    If Darwinism is wrong, Atheists shouldn’t be using it, and Christians should be leaving the faith because of Darwinism.

    There have been pro-ID atheists like Hoyle (who by the way used the phrase Intelligent Design long before Pandas and People) who reject Darwinism.

    Unless God opens someones eyes and heart, they cannot see. If they are in a state of blindness, its “reasonable” that they don’t believe.

    One the other hand, what is at issue now is something far less esoteric. Matheson’s claim that it would be generous to say that there are only 12 introns that are known to have important function. That claim is demonstratbly false.

    Whether awareness of Matheson’s gaffe brings anyone reading closer to God I have nothing to say. But for sure, we have made the public aware of another Darwinist who can’t use science to support his assertions.

    Matheson’s assertion that it would be generous to say there are only functioning introns is a serious mistake.

  46. 46

    Toronto,

    You seem to labor under a misunderstanding. I put commenters of both sides in moderation for not being civil. There is no anti-ID moderation conspiracy. If folks get put into moderation it’s because they have been uncivil, whether they can come out of moderation just depends. The best policy is to not get yourself put into moderation. Once you’re there, I will reasonably consider whether someone should come out, or not. For the last time, you have a free exchange of ideas, I don’t care where they appear on the list of comments. Everyone starts out on an equal footing, just as everyone does in life, but that doesn’t mean some folks won’t go to jail for their bad behaviour. I wish no one acted contrary to civility, I really do, then I wouldn’t have to police everyone, but we know that’s not reality, so don’t imply that I have a bias for moderating those contrary to ID, I moderate those contrary to civility, and I don’t appreciate the insinuation otherwise.

  47. 47
    San Antonio Rose

    I thought I read somewhere that comments were open at Matheson’s blog. Maybe we should take the fight to him.

    And when I say “we”, I mean “you” since I am not as knowledgeable as all y’all.

  48. Clive Hayden @ 46,

    Don’t think you’re only talking to me about this, it’s everyone that’s in that queue and everyone who has been banned.

    Why should Steve Matheson come back?

  49. Matheson is behind the times, you’d think he’d spool up on the developments of the ENCODE project. It’s amazing how prophetic the following report in 2008 accurately describes Matheson’s present day claims:

    Junking the idea of Junk DNA

    That hubristic notion—that just because the brightest minds in molecular biology couldn’t work out what much of the genome did, therefore it was junk

    Sound Familiar? :-)

    That hubristic notion—that just because the brightest minds in molecular biology couldn’t work out what much of the genome did, therefore it was junk—gets soundly knocked on the head by the paper at #4. A massive team called the ENCODE Project Consortium took a detailed look at a small part of the human genome and in so doing upset all kinds of preconceived ideas.

    ENCODE, as the name embodies, set out to create an Encyclopedia Of DNA Elements.

    One big surprise is that the human genome is, as the team puts it, “pervasively transcribed.” It had been thought that only coding regions and regulatory sequences were turned into RNA. In fact, almost every base in the sequence is associated with at least one piece of RNA. Many of the newly identified pieces of RNA extend transcripts well beyond the stretch that codes for a given gene. Many of the new non-protein-coding sequences discovered are from regions of the genome that, until now, had been thought to be mute. And many of the new transcripts overlap existing regions that do code for proteins.

    Another surprise is just how many transcription start sites there are. There are start sites just upstream of genes, obviously, but there are also many others throughout the genome, which could at least partly explain why so much of the DNA is in fact transcribed into RNA. These additional start sites share some characteristics with the promoter sites upstream of genes, but they differ in significant ways too, which indicates different functions that have yet to be elucidated.
    ….

    Some of those [DNA regions] may turn out to be functional in some cell types and under some circumstances that just happen not to have been studied to date.

    …..
    If the larger effort is as successful as the pilot study, molecular biologists, faced with the increased complexity of an ever-deepening understanding of the genome, may find themselves pining for the days when 99% of the sequence could be dismissed as junk

    Of note:

    Some of those [DNA regions] may turn out to be functional in some cell types and under some circumstances that just happen not to have been studied to date.

    What have I been harping about: biologist cite isolated cases where a cell has a feature that it doesn’t use and then he says “see that feature has no function”.

    That’s about as illogical as saying some of the ports on your computer have no function design because they aren’t being currently used or that a spare tire has no function because it is sitting in the trunk of a car.

  50. Clive Hayden @ 46,

    StephenB said I would probably have defended Hitler at Nuremberg.

    Is that civil?

  51. 2008 is so, like, yesterday.

    From this report:

    Moreover, the proportion of the genome that is transcribed in any given cell type remains an open question: results from “tiling” microarray analyses suggest that transcription is pervasive and that most of the genome is transcribed, whereas new deep sequencing-based methods suggest that most transcripts originate from known genes. We have addressed this discrepancy by comparing samples from the same tissues using both technologies. Our analyses indicate that RNA sequencing appears more reliable for transcripts with low expression levels, that most transcripts correspond to known genes or are near known genes, and that many transcripts may represent new exons or aberrant products of the transcription process. We also identify several thousand small transcripts that map outside known genes; their sequences are often conserved and are often encoded in regions of open chromatin. We propose that most of these transcripts may be by-products of the activity of enhancers, which associate with promoters as part of their role as long-range gene regulatory sites. Overall, however, we find that most of the genome is not appreciably transcribed.

    It’s not like this is all new.

    Then there’s the fact that all of the “functional” intronic sequences that people are finding barely make a dent in the amount of total intron-encoding DNA in the human genome. Add it all up and we’re still staring at a whole lotta junk. I explained this on the other thread on the subject.

  52. Mr Hayden,

    I moderate those contrary to civility, and I don’t appreciate the insinuation otherwise.

    Right. StephenB spreads the Easter message by calling one group of Jews psychotic, another group of Jews neurotic, then repeats the calumny that together they killed Christ, an anti-semitic slur that even his own church has repudiated. I call him on it with “Your Savior and His Mom say thanks.” Now which of us is in moderation?

    I know that you do put ID-friendly participants in moderation. I know you’ve put the brakes on Joseph when he’s over the line on bluster, when BA^77 goes off on some tangent and spams every thread with a YouTube video. And I know that moderating this site must be very time consuming and a pretty much thankless task. But I do think you’ve been inconsistent in some decisions.

  53. 53

    Clive Hayden @46:

    Toronto,

    You seem to labor under a misunderstanding. I put commenters of both sides in moderation for not being civil.

    Yet I’ve been placed in moderation without any notice that I’ve been uncivil. (How do you define incivility?)

    Please clarify.

  54. 54
  55. Art cited:

    most transcripts originate from known genes.

    First of all, I’d like to thank Dr. Hunt for appearing. I’ve had a history of exchanges with Dr. Hunt over the years and some were not so cordial.

    I’m deeply appreciative of the fact that despite this he is providing important technical information.

    That said, I have no problem with the majority of transcripts coming from known genes if we are talking PHYSICAL transcripts. However, we have the issue of the VARIETY of transcripts.

    I state again an important analogy:

    Say we have 1000 cars, 900 of them are identical, but 100 of them are unique, and the unique cars emerged out of Alternative Manufacturing (Splicing if you will). Thus we have 101 different kinds of cars, and 100/101 = 99% emerged via Alternative Splicing.

    Thus even though 90% of the physical cars did not go through alternative splicing, 99% of the VARIETY of cars went through alternative splicing (so to speak).

    We have to be careful in how we classify something as functioning or transcribed. Do we mean NEVER transcribed in a certain way, or sometimes transcribed in a few select instances in a few select cell types.

    If the paper is talking about known physical transcripts in known cell types (versus an exhaustive search of all 1,000,000,000,000 positionally differentiated cell types), then this paper does not necessarily invalidate the claims of ENCODE.

    To quote Francis Collins:

    “I’ve stopped using the term [junk DNA],” Collins said. “Think about it the way you think about stuff you keep in your basement. Stuff you might need some time. Go down, rummage around, pull it out if you might need it.”

    Finally, I have to take issue with a sweeping claim that something is NEVER transcribed. The human being has a long life and passes through many developmental stages. If indeed there are 1,000,000,000,000 positionally differentiated cell types, how can we definitely claim a particular alternative splice NEVER happens and is NEVER used without an exhaustive search of the behavior of all 1,000,000,000,000 positionally differentiated cell types?

    Also, we also know that introns aren’t necessarily just involved in Alternative Splicing, Sternberg points out there are more functions for them.

    My take is that it is extremely premature to say something is junk. It is certainly not ludicrous to hypothesize these regions have function.

  56. —Nakashima: “Right. StephenB spreads the Easter message by calling one group of Jews psychotic, another group of Jews neurotic, then repeats the calumny that together they killed Christ, an anti-semitic slur that even his own church has repudiated. I call him on it with “Your Savior and His Mom say thanks.” Now which of us is in moderation?”

    Would you care to back up that slanderous statement?

  57. here is article Dr. Fazale Rana just released on the splicing code that gives a inkling of the complexity being dealt with:

    Splicing Together the Case for Design, Part 2 (of 2) – Fazale Rana – June 2010
    Excerpt: Remarkably, the genetic code appears to be highly optimized, further indicating design. Equally astounding is the fact that other codes, such as the histone binding code, transcription factor binding code, the splicing code, and the RNA secondary structure code, overlap the genetic code. Each of these codes plays a special role in gene expression, but they also must work together in a coherent integrated fashion. The existence of multiple overlapping codes also implies the work of a Creator. It would take superior reasoning power to structure the system in such a way that it can simultaneously harbor codes working in conjunction instead of interfering with each other. As I have written elsewhere, the genetic code is in fact optimized to harbor overlapping codes, further evincing the work of a Mind.
    http://www.reasons.org/splicin.....n-part-2-2

    Well Nakashima you seem quite upset at my using videos in my posts. Yet most of my youtube/metacafe videos deal directly with the topic I’m on, but I do put other videos up if it is somewhat in harmony with the tone of the thread. Such as this one:

    Cool Hand Luke “Failure To Communicate.”
    http://www.youtube.com/watch?v=l_aVuS7cOIQ

  58. 58

    StephenB,

    Yes I’m interested in him backing it up too, I don’t remember such characterizations by you at all.

  59. Clive, in keeping with your question, here is a point I have alluded to in the past:

    The Sadducees and The Pharisees, did indeed, plot to kill Jesus Christ. That is a simple fact of history. The Catholic Church has never repudiated that fact because it isn’t in the business of repudiating facts. What the Church condemned was the idea that the Jews as a race were responsible for Christ’s death. It wasn’t the Jewish people who committed deicide; it was the Jewish and Roman leaders. It is ridiculous to persecute a race in the twentieth century or in any century for something that a small group of privileged leaders did 2000 years ago. To say the “Jews” were responsible for Christ’s death would be the equivalent of saying that the “Romans” were responsible for Pontius Pilate’s acts of cowardice. Get it Nakashima? Probably not!

    What was remarkable about the arrangement between the Sadducees and the Pharisees was their temporary truce, given the fact that they not only hated each other but were also, in fact, psychological opposites.

    The Sadducees were glued to the world, disbelieving in an afterlife, and prone to hate all forms of religion, especially the presumptuous variety offered by the Pharisees. Indeed, they were so morally lax and as to be neurotic. They loved change for the sake of change even when no change was needed.

    By contrast, the Pharisees found excessive fault with the world to which the Sadducees were glued and embraced rituals and forms at the expense of the natural moral law. (Notice I didn’t say “Jews.”) In complete contrast to the Sadducees, the Pharisees, were so rigid as to hate all change, even the kinds of change that are needed for progress. Sort of like radical Islamists. (Notice I didn’t say Muslims). If one group tends to love change for the sake of change, even when no change is needed, it exhibits signs of neurosis; if another group tends to hate all change, especially the kinds of change that are needed for progess, it exhibits traits of psychosis. Get it Nakashima? Probably not!

    Thus, and this is the point I once made, when two mortal enemies who would normally be inclined to destroy each other, and who would normally find it impossible to co-exist, call a temporary truce in order to form an alliance to kill a third person, that is a remarkable event which speaks of hatred at another level. It would be the equivalent of radical Islam [recognize the rigidity?] forming an alliance with atheist Darwinists [recognize the laxity?] to take out the Christians. Come to think of it, that isn’t a bad description of a current political phenomenon.

    On the other hand, Nakashima has stated that I claimed that one group of “Jews” was psychotic, likely knowing that I never did and never would use such anti-Semitic language. Thus, his remarks were inaccurate and reckless. As I have stated so often, Darwinists have a terrible time with context.

  60. To say the “Jews” were responsible for Christ’s death would be the equivalent of saying that the “Romans” were responsible for Pontius Pilate’s acts of cowardice. Get it Nakashima? Probably not!

    oh, I agree. You can’t use collective nouns to assign responsibility. The Jews did not crucify Christ. The Romans did not crucify Christ. Pilate crucified Christ.

    Of course, we can’t use collective nouns for “X plotted to kill Jesus”, either. The plot was the act of individuals. The Pharisees did not plot to kill Jesus. Some individual Pharisees plotted to kill Jesus.

    Of course, “plotted to kill” and “crucify” – ie sucessfully killing – are also different. Your previous statement was that two collective groups crucified Jesus.

  61. 61

    Nakashima,

    I’m going to stop this threadjacking, as you put it, in it’s place right now. No more discussion of the Pharisees and Sadducees. This was, if you recall, an offshoot discussion of my moderating, which was, itself, an attempt at threadjacking. Let’s keep the topic on the thread topic.

  62. Clive,

    You asked for the evidence:

    StephenB,

    Yes I’m interested in him backing it up too, I don’t remember such characterizations by you at all.

    The least you can do is to let it appear. Otherwise you are allowing StephenB’s baseless accusation of slander to stand.

    Here’s the relevant comment from StephenB on March 31st:

    Lawless neurotics [surprisingly they are like legalistic psychotics in the sense that they seek to tyrannize as soon as they gain power], who hated the Declaration of Independence and the idea of God as a lawgiver, set out to change that absolute standard into the relative and unstable standard of law by popular opinion and judicial fiat, and, for the most part, they have been successful. Their strategy was to characterize advocates of the natural moral law, which is the rational midpoint between two extremes, as legalistic psychotics. Meanwhile, real legalistic psychotics have been stumping for Sharia Law and their lawless counterparts, though their total opposites, encourage this because they hope that, as a coalition, they can team up to destroy the Judeo/Christian formulation and form a new ruling class, much like the psychotic Pharasees and the neurotic Sadducees, who temporarily put aside their mutual hate to crucify who they hated even more.

  63. 63

    pelagius,

    Fair enough, but StephenB has already answered this, anticipating yours and Nakashima’s difficulty with context. This is the last of it, from now on let’s keep the comments on topic please.

  64. 64

    Wow.

    You ID opponents must have had a severe upwelling of righteous indignation when Miller went on the radio and said if ID has its way all medical advancement will come to a stop. Yes, ID will kill your babies. Or when Dawkins uses descriptors like “insane”. Or when Moran says Liars for Jesus, or Matheson says just plain liars without even a hope of integrity.

  65. Wow.

    You ID opponents must have had a severe upwelling of righteous indignation when Miller went on the radio and said if ID has its way all medical advancement will come to a stop.

    You bet I did when I hear that accusation.

    Matheson is labeling people that think introns have function as “driniking kool aid”. I’ve listed several mainstream pappers that link disease to intron malfunction. You’d think he’d be a little more circumspect in light of the fact such accusations also insult the work of these scientists who are making medical advances.

    Pellionisz is an ID sympathizer of sorts (unorthodox ID), and he had this to say:

    uncounted millions of people died miserable deaths while scientists were looking for the “gene” causing their illnesses – and were not even supposed to look anywhere but under the lamp illuminating only 1.3% of the genome (the genes)

    Pellionisz also mentione the ABC News Documnetary that was not aired in the US (where it is not politically correct to advocated junk DNA research, as evidence by Matheson and Ken Miller’s prejudice), but did air elsewhere in the world.

    The documentary included Mattick and an equally important pioneer of Junk DNA research, Malcom Simons.

    Here is a link to that documentary:
    Genius of Junk

  66. —Steve Matheson: “It needs to be destroyed, and I will do what I can to bring that about.”

    Perhaps you can begin by suing Stephen Meyer for dueling with an unarmed man.

  67. StephenB @ 66,

    —Steve Matheson: “It needs to be destroyed, and I will do what I can to bring that about.”

    While at one time I would have said that reasoned discussion is the road to take against ID, I now agree with Steve Matheson.

    The Evo side has to engage ID organizations in the courts to prevent ID from getting into our schools.

    These organizations have to be shown for what they are, i.e., groups that promote a narrow focused world-view.

  68. 68

    Toronto,

    While at one time I would have said that reasoned discussion is the road to take against ID, I now agree with Steve Matheson.

    What would you do to bring the about the destruction of the Discovery Institute? I’ve asked the same question to Steve Matheson, and he hasn’t yet responded, so what is your response? I hope you realize that advocating destruction of the Discovery Institute qualifies you for banning, because if destruction isn’t incivility, then what is? But I’ll let you answer this one last question.

  69. Toronto-

    THe truth may seem like a narrow focused world-view. Is it narrow focused to think 1+1=2? Does every organization have to consider every possible world-viiew in order to exist? This seems absurd.

  70. 70

    The Discovery Institute must be destroyed for one and only one reason – the evidence for ID cannot be denied. It cannot be brushed aside, explained away, and falsified by evidence that doesn’t exist. Absolutely no one knows this better than a materialist, or even more striking, no one knows this better than a scientist. The training that empowers science is also the training that cannot ignore ID. The strategem that design in nature is obvious but not real didn’t come about by chance. ;-)

    Matheson is at wits end. He’s being practical.

  71. —Toronto: “These organizations have to be shown for what they are, i.e., groups that promote a narrow focused world-view.”

    Why not simply retract your statement agreeing that the Discovery Institute ought to be destroyed and acknowledge that you got carried away with your own rhetoric? Many of us on both sides have been guilty of pushing the envelope a bit too far at times.

  72. Toronto, in the midst of your and Matheson’s delusion for “Destroying the Discovery Institute”, do you favor making it a thought crime to even think Intelligent Design thoughts about the unparalleled complexity being discovered in life?:

    1984
    http://www.youtube.com/watch?v=z9PQ16KVntQ

  73. I share Matheson’s opinion of the Discovery Institute but he should have remembered Voltaire’s dictum: “I disagree with what you say but I will defend to the death your right to say it”

  74. 74

    “I share Matheson’s opinion of the Discovery Institute but he should have remembered Voltaire’s dictum…”

    Nothing like having it both ways, eh Seversky?

  75. 75

    Toronto,

    I asked you a question.

  76. Hey Guys, Stephen Meyer has a new video interview up at ENV:

    watch Stephen Meyer’s interview on the evidence for intelligent design, which aired Friday, June 18, on The 700 Club.

    Believing Life’s ‘Signature in the Cell’ an Interview with Stephen Meyer
    http://www.evolutionnews.org/2.....35911.html

  77. 77

    Toronto,

    You should take StephenB’s advice.

  78. Voltaire, and a little document called the Constitution.

  79. Hey Guys, Stephen Meyer has another interview with CBN up at ENV:

    http://www.evolutionnews.org/2.....35991.html

  80. Clive Hayden,

    I hope you realize that advocating destruction of the Discovery Institute qualifies you for banning, because if destruction isn’t incivility, then what is?

    While not addressed at me – I am no part of the debate in this thread, I just don’t see much of a difference between expressing a desire to dispose of DI, meaning the burial of the concept of Intelligent Design vs. the DI & UcD’s stated intention of destroying Darwinism?

  81. 81

    Cabal,

    Darwinism is a false science, the Discovery Institute is made up of people. Which one would you like to see destroyed?

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