25 Responses to “In Defense of Hidden Objectives”

1. Bilbo Says:
   June 17th, 2010 at 1:08 am

   Ah yes, by all means, let's add more fuel to the fire.

Comment by Bilbo — June 17, 2010 @ 1:08 am

2. Salvador T. Cordova Says:
   June 17th, 2010 at 1:24 am

   Ah yes, by all means, let's add more fuel to the fire.

   C'mon we're just having a little fun. Matheson and Moran are giving us some real howlers. Not to mention, Matheson's throwing a public tantrum:

   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</a.
   

   So he refers to the DI staff as a "cadre of dogs".

   In that case, maybe some of the UD authors too.

   Arf. Arf.

   Moran was screaming that ID proponents are idiots, especially for quoting the high number of Alternative Splices.

   Wells was keen to point out the high number cited by ID proponents was inspired by nine (count them, NINE) of Larry's own colleagues at University of Toronto. Talk about Larry making himself look like a ….. well I won't say it— but you know what mean.

Comment by Salvador T. Cordova — June 17, 2010 @ 1:24 am

3. olegt Says:
   June 17th, 2010 at 1:35 am

   Bradford wrote:
   

   Matheson and Moran have done us all a favor. Their arrogance, drawn from over confidence, has inspired some questionable statements as Salvador Cordova has drawn attention to in the comment section in another thread devoted in large part to silly analogies made by Matheson. The M&M boys may strut like they are 10 feet tall but their statements make them look small. They look more like peevish juveniles than infallible experts.

   This is insane.

Comment by olegt — June 17, 2010 @ 1:35 am

4. Salvador T. Cordova Says:
   June 17th, 2010 at 1:39 am

   Here is a double howler by Matheson:

   Chapter 4 and 5

   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,

   First howler:

   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. HOWLER. Did it ever occur to Matheson the functions could exist independent of whether we recognize them or no. HOWLER!

   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.

   We are aware more of the introns in more than just a dozen involved alternative splices. Do we have to actually spoon feed Matheson the list of known alternative splices? Do you think he could count beyond a dozen if we did so?

   Further, as Sternberg astutely observed:

   Then there are the regulatory codes associated with such RNA genes, which also occur in introns. And RNAs that emanate from introns but that are not part of messenger RNAs; 78,147 of them are known to exist in humans. Even if only ten percent of the latter RNAs play some role in cellular organization, we have far more than “a handful” of functional introns in this category alone.

   And there’s still more. RNA is essential for chromatin organization in the nucleus. When chromatin-associated RNA is degraded by experimental means, the geometry of chromosomes and nuclear metabolism is adversely affected. Yet a recent study of this class of RNAs in human cells revealed that over half of the transcripts (52%) are derived from… introns!

   I could go on. Various DNA control modules have been mapped to introns, including alternative promoters, enhancers, silencers, and nuclear matrix attachment sites—some of which influence genes that are located over a million basepairs away on the chromosome. But sorting through all the studies that have been published on this subject would be a big job.

   A job, obviously, that Matheson has not done—though whether through ignorance, sloth, or duplicity I cannot say.

Comment by Salvador T. Cordova — June 17, 2010 @ 1:39 am

5. Salvador T. Cordova Says:
   June 17th, 2010 at 1:56 am

   Let's help matheson count to a dozen starting with a list that Art Supplied:

   Schöning JC, Streitner C, Meyer IM, Gao Y, Staiger D.
   Reciprocal regulation of glycine-rich RNA-binding proteins via an interlocked feedback loop coupling alternative splicing to nonsense-mediated decay in Arabidopsis.
   Nucleic Acids Res. 2008 Nov 4. [Epub ahead of print]

   Dinkins RD, Majee SM, Nayak NR, Martin D, Xu Q, Belcastro MP, Houtz RL, Beach CM, Downie AB.
   Changing transcriptional initiation sites and alternative 5'- and 3'-splice site selection of the first intron deploys Arabidopsis protein isoaspartyl methyltransferase2 variants to different subcellular compartments.
   Plant J. 2008 Jul;55(1):1-13.

   Puyaubert J, Denis L, Alban C.
   Dual targeting of Arabidopsis holocarboxylase synthetase1: a small upstream open reading frame regulates translation initiation and protein targeting.
   Plant Physiol. 2008 Feb;146(2):478-91.

   Bove J, Kim CY, Gibson CA, Assmann SM.
   Characterization of wound-responsive RNA-binding proteins and their splice variants in Arabidopsis.
   Plant Mol Biol. 2008 May;67(1-2):71-88.

   Bocobza S, Adato A, Mandel T, Shapira M, Nudler E, Aharoni A.
   Riboswitch-dependent gene regulation and its evolution in the plant kingdom.
   Genes Dev. 2007 Nov 15;21(22):2874-9.

   Muralla R, Chen E, Sweeney C, Gray JA, Dickerman A, Nikolau BJ, Meinke D.
   A bifunctional locus (BIO3-BIO1) required for biotin biosynthesis in Arabidopsis.
   Plant Physiol. 2008 Jan;146(1):60-73.

   Zhang XC, Gassmann W.
   Alternative splicing and mRNA levels of the disease resistance gene RPS4 are induced during defense responses.
   Plant Physiol. 2007 Dec;145(4):1577-87.

   Rossignol P, Collier S, Bush M, Shaw P, Doonan JH.
   Arabidopsis POT1A interacts with TERT-V(I8), an N-terminal splicing variant of telomerase.
   J Cell Sci. 2007 Oct 15;120(Pt 20):3678-87.

   Castells E, Puigdomènech P, Casacuberta JM.
   Regulation of the kinase activity of the MIK GCK-like MAP4K by alternative splicing.
   Plant Mol Biol. 2006 Jul;61(4-5):747-56.

   Lee JR, Jang HH, Park JH, Jung JH, Lee SS, Park SK, Chi YH, Moon JC, Lee YM, Kim SY, Kim JY, Yun DJ, Cho MJ, Lee KO, Lee SY.
   Cloning of two splice variants of the rice PTS1 receptor, OsPex5pL and OsPex5pS, and their functional characterization using pex5-deficient yeast and Arabidopsis.
   Plant J. 2006 Aug;47(3):457-66.

   de la Fuente van Bentem S, Vossen JH, Vermeer JE, de Vroomen MJ, Gadella TW Jr, Haring MA, Cornelissen BJ.
   The subcellular localization of plant protein phosphatase 5 isoforms is determined by alternative splicing.
   Plant Physiol. 2003 Oct;133(2):702-12.

   Savaldi-Goldstein S, Aviv D, Davydov O, Fluhr R.
   Alternative splicing modulation by a LAMMER kinase impinges on developmental and transcriptome expression.
   Plant Cell. 2003 Apr;15(4):926-38.

   Jasinski S, Perennes C, Bergounioux C, Glab N.
   Comparative molecular and functional analyses of the tobacco cyclin-dependent kinase inhibitor NtKIS1a and its spliced variant NtKIS1b.
   Plant Physiol. 2002 Dec;130(4):1871-82.

   Macknight R, Duroux M, Laurie R, Dijkwel P, Simpson G, Dean C.
   Functional significance of the alternative transcript processing of the Arabidopsis floral promoter FCA.
   Plant Cell. 2002 Apr;14(4):877-88.

   Dinesh-Kumar SP, Baker BJ.
   Alternatively spliced N resistance gene transcripts: their possible role in tobacco mosaic virus resistance.
   Proc Natl Acad Sci U S A. 2000 Feb 15;97(4):1908-13.

   Zhou DX, Kim YJ, Li YF, Carol P, Mache R.
   COP1b, an isoform of COP1 generated by alternative splicing, has a negative effect on COP1 function in regulating light-dependent seedling development in Arabidopsis.
   Mol Gen Genet. 1998 Feb;257(4):387-91.

   That's about 17 (more than a dozen), can Matheson count that high? Hahaha.

   PS
   Of course we have to establish introns were surely involved (versus just likely to be involved), but I'm sure we can find examples where introns are known to be involved.

Comment by Salvador T. Cordova — June 17, 2010 @ 1:56 am

6. Salvador T. Cordova Says:
   June 17th, 2010 at 2:01 am

   The above list of course were for a particular plant, but I'm sure we could do the same for humans. We have 20,000 genes in humans (only fraction of which we've studied in depth). But do we have to actually go through a similar exercise for Matheson to count to a higher number than 12?

Comment by Salvador T. Cordova — June 17, 2010 @ 2:01 am

7. Salvador T. Cordova Says:
   June 17th, 2010 at 2:35 am

   Let's spoon feed matheson to more than a dozen. There are estimated at least 190,000 introns (by Matheson's own count which by the way disagrees with Moran's count of 150,000).

   From wiki on introns, here is a reasonble example of one important intron:

   Introns may also contain "old code", or sections of a gene that were once translated into a protein, but have since become inactive. It was generally assumed that the sequence of any given intron is junk DNA with no biological function. More recently, however, this is being disputed.[5] For example, 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 one, eleven to go….

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

   That's 2, 10 to go

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

   That's 3, 9 to go…

   http://www.jneurosci.org/cgi/c... Retention Is Upregulated in Amyotrophic Lateral Sclerosis and Associated with Disease Pathology

   That's 4, 8 to go

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

   That's 5, 7 to go

   …..

   you get the picture I hope.

   I've listed a mere 5 genes (a number even Matheson can count up to), but there are 20,000. Is matheson so sure we'll never find more important roles for introns in all these 20,000 genes 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.

Comment by Salvador T. Cordova — June 17, 2010 @ 2:35 am

8. Salvador T. Cordova Says:
   June 17th, 2010 at 2:47 am

   Bergmann lists about 9 more introns with imortant roles:
   http://www.rae.org/introns.htm...

   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.

   And there are how many introns? 190,000. How difficult it was to elucidate function for even 1 intron, much less the other 190,000.

   At the very least, I've listed about 14 and I could go on. It doesn't give a nice picture for Matheson who claims a "dozen" is "generous". Ha!

Comment by Salvador T. Cordova — June 17, 2010 @ 2:47 am

9. ID guy Says:
   June 17th, 2010 at 7:28 am

   Yes olegt, it is insane for two alleged scientists (Moran & Matheson) to not understand the science they are supposed to be defending.

   This episode reminds me of the South Park episode in which Dawkins falls for "Mrs" Garrison and Eric Cartman freezes himself and gets revived in the 26th century.

   Science rules the day- everyone is an atheist and the debate is about what to call themselves.

   "Science damn you!" (As opposed to "God damn you")

Comment by ID guy — June 17, 2010 @ 7:28 am

10. ully Says:
    June 17th, 2010 at 8:09 am

    Isn't it a bit hypocritical to complain about the nastiness of some ID critics in such a nasty way?

    Mr Cordova in particular should be ashamed for hiding behind the ban hammer at UD when he can address the offending critics directly at their own uncensored blogs.

Comment by ully — June 17, 2010 @ 8:09 am

11. Bradford Says:
    June 17th, 2010 at 8:38 am

    Mr Cordova in particular should be ashamed for hiding behind the ban hammer at UD when he can address the offending critics directly at their own uncensored blogs.

    You should be ashamed for this comment. The critics can come here as you have. You've been here before haven't you?

Comment by Bradford — June 17, 2010 @ 8:38 am

12. Salvador T. Cordova Says:
    June 17th, 2010 at 10:33 am

    Isn't it a bit hypocritical to complain about the nastiness of some ID critics in such a nasty way?

    I wasn't complaining about Matheson's nastiness, I thought it was kind of funny.

Comment by Salvador T. Cordova — June 17, 2010 @ 10:33 am

13. ID guy Says:
    June 17th, 2010 at 10:54 am

    ully:
    Isn't it a bit hypocritical to complain about the nastiness of some ID critics in such a nasty way?

    Do unto others as they do unto you- or something like that.

Comment by ID guy — June 17, 2010 @ 10:54 am

14. Salvador T. Cordova Says:
    June 17th, 2010 at 11:04 am

    I'm really not complaing about Matheson. Personally I hope Matheson turns into anoterh Abbie Smith. He'll be a rich source of future quotations.

    By the way here are more cases where intron are implicated to function:

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

    and

    A deep intronic mutation in the RB1 gene leads to intronic sequence exonisation

    and

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

    and

    Trinucleotide Mutation Friedriech Ataxia

    Um, can Matheson count beyond 12?

Comment by Salvador T. Cordova — June 17, 2010 @ 11:04 am

15. olegt Says:
    June 17th, 2010 at 11:37 am

    Salvador T. Cordova wrote:
    

    Personally I hope Matheson turns into anoterh Abbie Smith.

    That seems like a perverse desire on your part, Sal. Your skirmish with Abbie had some interesting consequences. If I remember correctly, one of you had to apologize and withdraw from blogging for a while. Can't recall which one.

Comment by olegt — June 17, 2010 @ 11:37 am

16. Bradford Says:
    June 17th, 2010 at 12:48 pm

    Anyhow, the first 15 minutes they talk about epigenetics, the Altenberg 16 conference, Susan Mazur, and try to downplay the Altenberg theme that evolutionary biology is in a vast state of disarray. Abbie lets us know how little she understands epigenetics and is evidently still laboring under the outdated Dawkins era notion that genes and proteins are everything. PZ, who is more up on the subject, looks a bit aghast after Abbie describes her understanding of epigenetics. If Abbie had been one of us he’d have called her an idiot but since she’s on his side he gently tried to correct her, saying his students have the same misunderstandings and it’s difficult to teach. Abbie rudely interrupts over and over as PZ attempts to explain.

    here

Comment by Bradford — June 17, 2010 @ 12:48 pm

17. Bradford Says:
    June 17th, 2010 at 1:12 pm

    The tone of the Stephen Meyer critiques specifically and ID critiques more generally tells us much. I never bought into the pretext of scientific outrage. After all it was not too long ago that a legitimate source of outrage arose in the form of climategate and ID critics were mute. The all about science mantra reveals a fundamental dishonesty of among critics. What really bothers them has nothing to do with science.

Comment by Bradford — June 17, 2010 @ 1:12 pm

18. Salvador T. Cordova Says:
    June 17th, 2010 at 3:48 pm

    In 2008, this prophetic report came out:

    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

    From Junking the idea of junk

    Sound familiar? Matheson is one of the brightest minds in molecular biology, he said so himself.

Comment by Salvador T. Cordova — June 17, 2010 @ 3:48 pm

19. Salvador T. Cordova Says:
    June 17th, 2010 at 4:40 pm

    Hey Bradford, Steve Matheson has something to say about us.

    He made this comment in reply to his open letter:

    I returned to see the high-class commentators of Telic Thoughts and Uncommon Descent waxing eloquent about introns and "junk DNA" with adolescent bravado toward me. I don't know what's more pathetic: the constant redirection of the questions, or the monstrous hypocrisy of browbeating critics about their "tone."

    Where have I complained about Steve's tone?

    I thought it was especially entertaining in light of the gaffe's in his essays.

    One of the the question was, ahem, are there more than 12 introns that have function? Steve said a 12 would be a generous estimate. We have deftly demonstrated the contrary.

Comment by Salvador T. Cordova — June 17, 2010 @ 4:40 pm

20. Bradford Says:
    June 17th, 2010 at 5:17 pm

    Matheson: I returned to see the high-class commentators of Telic Thoughts and Uncommon Descent waxing eloquent about introns and "junk DNA" with adolescent bravado toward me. I don't know what's more pathetic: the constant redirection of the questions, or the monstrous hypocrisy of browbeating critics about their "tone."

    Salvador: Where have I complained about Steve's tone?

    I mentioned the word tone in a comment. "Adolescent bravado" looks like tit for tat for the phrase "peevish juveniles" which appears in the OP.

Comment by Bradford — June 17, 2010 @ 5:17 pm

21. ully Says:
    June 17th, 2010 at 7:20 pm

    Bradford:

    You should be ashamed for this comment. The critics can come here as you have. You've been here before haven't you?

    Why would you think I have been here before? I have actually just lost my "TT virginity" so to speak. If my style reminds you of someone, well I am sure it's just a coincidence, just like the resemblance between ID guy's style and substance and that of Joe G is just a coincidence. Great minds think alike and sometimes they write alike as well.

    Anyway, I thank you sincerely for allowing me to post here. Many ID blogs, such as UD, are notorious for banning even the most polite critics. I'm glad this blog is different.

Comment by ully — June 17, 2010 @ 7:20 pm

22. Bradford Says:
    June 17th, 2010 at 8:08 pm

    If my style reminds you of someone, well I am sure it's just a coincidence, just like the resemblance between ID guy's style and substance and that of Joe G is just a coincidence. Great minds think alike and sometimes they write alike as well.

    Are you claiming greatness analogous to Joe G?

Comment by Bradford — June 17, 2010 @ 8:08 pm

23. ully Says:
    June 17th, 2010 at 8:41 pm

    Nobody even comes close to Joe G's greatness. Except perhaps for some great prophets in the distant past. So no – I humbly accept my place at the feet of Joe G.

Comment by ully — June 17, 2010 @ 8:41 pm

24. ID guy Says:
    June 18th, 2010 at 10:04 am

    ully:
    If my style reminds you of someone, well I am sure it's just a coincidence, just like the resemblance between ID guy's style and substance and that of Joe G is just a coincidence.

    No, it's not a coincidence.

    As I have said already it is by design…

Comment by ID guy — June 18, 2010 @ 10:04 am

25. мурино оборонная « Блоголента Says:
    July 15th, 2010 at 12:13 pm

    [...] Bradford пишет: You can follow any responses to this entry through the RSS 2.0 feed. You can leave a response, or trackback from your own site. The trackback link is: http://telicthoughts.com/in-de... ….. Evidence for a calcium regulated, bidirectional intronic promoter in the murine TCR V1 gene. and. Trinucleotide Mutation Friedriech Ataxia. Um, can Matheson count beyond 12? Comment by Salvador T. Cordova — June 17, 2010 @ 11:04 am … [...]

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