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derwood

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Lester wrote:

"Evolution is good for nothing, it holds real science back with garbage concepts like “Junk DNA”."


This is an old canard tossed out by YECs and IDists and sundry anti-evolution types - that because 'we' labelled noncoding DNA 'junkDNA' based on our materialistic worldview/paradigm, all sorts of research was not done on this DNA and by golly, it really ISN'T junk!  Just as YEC/ID have claimed all along.


The problem with that position is that, frankly, it is all lies and disinformation.

The following is an email exchange I had with a 'biggie' at the Discovery Institute.  As I've not gotten permissions, I am removing the names.

If you don't believe that this exchange took place, I can email you the unedited version.

In chronological order, starting with my initial inquiry:

***

Greetings,

I recently read an account of a talk by [creationist/IDist] and it was stated  that he [creationist/IDist] had indicated that Bill Dembski had predicted function in junk DNA 10 years ago.
I was wondering if you could shed some light on this - where this prediction was made, etc.

Thank you,

[me]

***
---Original Message---


Dear Prof. [me]:

Bill Dembski made the prediction in various lectures in the latter half of the 1990s. I believe that the earliest published version was in an essay in First Things published in 1998, where Dembski wrote:

Consider the term "junk DNA." Implicit in this term is the view that because the genome of an organism has been cobbled together through along, undirected evolutionary process, the genome is a patchwork of which only limited portions are essential to the organism. Thus on an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function. And indeed, the most recent findings suggest that designating DNA as "junk" merely cloaks our current lack of knowledge about function. For instance, in a recent issue of the Journal of Theoretical Biology, John Bodnar describes how "non-coding DNA in eukaryotic genomes encodes a language which programs organismal growth and development." Design encourages scientists to look for function where evolution discourages it.


The full text of the article is available at http://www.discovery.org/a/62.

[creationist/IDist]

***
On Mar 3, 2009, at 6:05 AM, [me]wrote:

Dear Dr. [creationist/IDist],

Thank you for your prompt reply.

The claim that advocates of ID or Creationism had made such predictions have been floating about for some time and I have never been able to ascertain their veracity.

However, it seems that functions in so-called junk DNA had been not just predicted and speculated about by evolutionary biologists well before 1998, but in fact function in some such DNA had been experimentally discovered as early as 1975:

Cell. 1975
Feb;4(2):107-11.

The general affinity of lac repressor for E. coli DNA: implications for gene regulation in procaryotes and eucaryotes.

By equilibrium competition experiments, the dissociation constant (K(RD)) of lac repressor for E. coli DNA carrying a deletion of the lac operon was measured at a variety of salt concentrations. These data are used in the consideration of several aspects of protein-DNA interaction: Quantitative estimates of specificity are made. Specificity changes only slightly with salt concentration. We calculate that in vivo, 98 percent or more of repressor is bound to DNA predominately at sites other than the lac operator. Inducers shift repressor from operator to nonoperator DNA, but do not free it from DNA. The general affinity of repressor for E. coli DNA is sufficient to support a model where repressor slides along DNA for significant distances. The effective dissociation constant of repressor for operator (K(eff)) is very sensitive to the total DNA concentration. We propose that "junk" DNA in eucaryotes functions to maintain total DNA at an optimum concentration. We consider the lac operon in the nucleus of a lymphocyte, point out that severe difficulties would be encountered, and suggest possible solutions.


Or Zuckerkandl from 1981:
A general function of noncoding polynucleotide sequences

Abstract
  It is proposed that a general function of noncoding DNA and RNA sequences in higher organisms (intergenic and intervening sequences) is to provide multiple binding sites over long stretches of polynucleotide for certain types of regulatory proteins. Through the building up or abolishing of high-order structures, these proteins either sequester sites for the control of, e.g., transcription or make the sites available to local molecular signals. If this is to take place, the existence of a c-value paradox becomes a requirement. Multiple binding sites for a given protein may recur in the form of a sequence motif that is variable within certain limits. Noncoding sequences of the chicken ovalbumin gene furnish an appropriate example of a sequence motif, GAAAATT. Its improbably high frequency and significant periodicity are both absent from the coding sequences of the same gene and from the noncoding sequences of a differently controlled gene in the same organism, the preproinsulin gene. This distribution of a sequence  motif is in keeping with the concepts outlined. Low specificity of sequences that bind protein is likely to be compatible with highly specific conformational changes.


There are many others predating the 1990s.  A cursory Medline search would have revealed these.  It seems then that Mr.Dembski's claim, "Design encourages scientists to look for function where evolution discourages it" is somewhat of an embellishment, for I am quite certain that Zuckerkandl, at least, is not an advocate for ID or any other form of creationism.

Thank you again for your reply.

Sincerely,

[me]

***

[me],

Certainly there were a few biologists who went against the consensus view of evolutionary biology during the past few decades (and Dembski himself cites one of these in his article). The fact remains that the junk DNA paradigm was nurtured, inspired, and sustained by Neo-Darwinism, as biologist Richard Sternberg documents in his article "On the Roles of Repetitive DNA Elements in the Context of a Unified Genomic– Epigenetic System," Annals of the New York Academy of Sciences, Vol. 981: 154–188 (2002).  The progress made in deciphering function in junk DNA was largely in spite of Neo-Darwinism, not because of it. At the same time, when ID theorists proposed function for "junk DNA" they were scorned or repudiated by the proponents of Neo-Darwinism. You might also read the article at [http://www.ideacenter.org/contentmgr/showdetails.php/id/1437], which provides further documentation and cites the example of a rejected letter submitted to Science by ID proponent Forrest Mims in 1994 about function in "junk DNA."

Sincerely,

[creationist/IDist]
***

Hello [creationist/IDist],

Thank you for the additional information, though I do not think it helps the ID 'prediction' case much.  A quick perusal of the Sternberg paper shows that he did not cite either of the papers I mentioned previously, both written by adherents of 'neo-Darwinism' and both published well before either Mims' letter (how many letters are rejected by Science, do you suppose?) or Dembski's 'First Things' essay or Luskin's public relations essay.  

Further, evolutionary biologist T. Ryan Gregory has amassed a lengthy collection of citations and quotes from the 1970s and beyond documenting the fact that despite the "public" understanding of what junk DNA is, that biologists took for granted (his words) that at least some such DNA has function (http://genomicron.blogspot.com/2008/02/junk-dna-quotes-o-interest-series.html; this page: http://genomicron.blogspot.com/2008/02/quotes-of-interest-beware-single.html is also very important as a cautionary tale).  
Gregory's site also lists quotes/citations in which function for certain DNA elements was considered and even looked for but not found (i.e., there really is some 'junk' DNA, and it was not just assumed to be 'junk'- that was a conclusion).

Cross-checking Sternberg's references with those compiled by Gregory indicates that exactly 1 of them are to be found in Sternberg's list.  I do not know exactly how many such citations Gregory's site has (I stopped counting at 25 and I did not count press releases and the like), and it is not exhaustive, but it shows quite clearly that mainstream researchers were actively looking into these issues, not dismissing them.

In the end, what I found 'unpalatable' about Sternberg's paper was the fact that it appears to me that he cherry-picked papers to prop up his position, especially in light of his focusing on satellite DNA and LINES and SINES - Gregory documents pretty well that despite Sternberg's conclusions, 'neo-Darwinism' adherents were the ones speculating about and identifying the possible functions of these elements (Britten, for example, postulated function of tandem repeats as early as 1968 - more than 30 years before Sternberg claims that we all just said it was 'junk') long before the ID adherents (and some under-informed science writers and, sadly, even some under-informed biologists) tried to claim primacy in merely "predicting" the notion that there is function in them (I note that there is no actual research by ID/creationism advocates to be found on the subject, just a lot of after-the-fact historical revisionism).

In the end, I think it is documentable and pretty clear that tales of neo-Darwinism putting the brakes on such research is ultimately nonsense, fueled in part by an unfortunate use of misinterpreted terminology and a failure of many writers to adequately understand and research the material prior to writing about it.

Sincerely,

[/me]

***

[creationist/IDist] stopped corresponding with me at that point.

I think that it is documented (above, for example) that the YEC/ID claims that evoluton 'stifled' research on 'junkDNA' is totally bogus, and yec/ID claims that creationists/IDists had 'predicted' function in junkDNA is just a reflection of either their hubris or their ignorance of the literature.

What say you, Lester?




-------
Lester:

"I said I have a doctorate and a university background in anatomy, physiology, biochemistry, physics, chemistry, pathology etc. ..."
 


Posts: 1646 | Posted: 4:53 PM on October 21, 2009 | IP
orion

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Derwood - very enlightening post.  You do, indeed, do your homework!  Thank you for sharing.
 


Posts: 1460 | Posted: 11:05 PM on October 21, 2009 | IP
derwood

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Quote from orion at 11:05 PM on October 21, 2009 :
Derwood - very enlightening post.  You do, indeed, do your homework!  Thank you for sharing.



Thanks,

I must say, however, that very little homework needed to be done to find out that the YEC/ID-types are really just embellishing and engaging in unwarranted exterapolations and su8ch when they say that we held up research and the like.  It was evolutionists that DID the research that discovered function in some noncoding DNA, not IDists ofr YECs (who basically refuse to test their claims - I'll be starting a new thread about that shortly).


-------
Lester:

"I said I have a doctorate and a university background in anatomy, physiology, biochemistry, physics, chemistry, pathology etc. ..."
 


Posts: 1646 | Posted: 08:20 AM on October 22, 2009 | IP
derwood

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A good related article:

junkDNA=junkRNA?




-------
Lester:

"I said I have a doctorate and a university background in anatomy, physiology, biochemistry, physics, chemistry, pathology etc. ..."
 


Posts: 1646 | Posted: 08:48 AM on October 22, 2009 | IP
wisp

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The fact remains that the junk DNA paradigm was nurtured, inspired, and sustained by Neo-Darwinism,
D'oh!



-------
Quote from Lester10 at 2:51 PM on September 21, 2010 in the thread
Scientists assert (by Lester):

Ha Ha. (...) I've told you people endlessly about my evidence but you don't want to show me yours - you just assert.
porkchop
Would we see a mammal by the water's edge "suddenly" start breathing underwater(w/camera effect of course)?
Contact me at youdebate.1wr@gishpuppy.com
 


Posts: 3037 | Posted: 09:40 AM on October 22, 2009 | IP
derwood

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Quote from wisp at 09:40 AM on October 22, 2009 :
The fact remains that the junk DNA paradigm was nurtured, inspired, and sustained by Neo-Darwinism,
D'oh!



Well see?  Evidence doesn't matter.  They've got their truth, and nothing will budge them from it.  Even evidence to the contrary.




-------
Lester:

"I said I have a doctorate and a university background in anatomy, physiology, biochemistry, physics, chemistry, pathology etc. ..."
 


Posts: 1646 | Posted: 10:06 AM on October 22, 2009 | IP
derwood

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Gee, I go to all this trouble to start a thread for Dr.Lester to tell us all about junkDNA and he's not replied once...


-------
Lester:

"I said I have a doctorate and a university background in anatomy, physiology, biochemistry, physics, chemistry, pathology etc. ..."
 


Posts: 1646 | Posted: 10:34 AM on October 26, 2009 | IP
Fencer27

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Junkie
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Quote from derwood at 10:34 AM on October 26, 2009 :
Gee, I go to all this trouble to start a thread for Dr.Lester to tell us all about junkDNA and he's not replied once...



Dr. Lester? What an oxymoron.


-------
"So in everything, do to others what you would have them do to you, for this sums up the Law and the Prophets." - Jesus (Matthew 7:12)
 


Posts: 551 | Posted: 10:56 AM on October 26, 2009 | IP
derwood

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Yup.


-------
Lester:

"I said I have a doctorate and a university background in anatomy, physiology, biochemistry, physics, chemistry, pathology etc. ..."
 


Posts: 1646 | Posted: 1:44 PM on October 30, 2009 | IP
derwood

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bump for the YEC PhD expert on all things....


-------
Lester:

"I said I have a doctorate and a university background in anatomy, physiology, biochemistry, physics, chemistry, pathology etc. ..."
 


Posts: 1646 | Posted: 5:36 PM on November 2, 2009 | IP
orion

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Quote from derwood at 10:34 AM on October 26, 2009 :
Gee, I go to all this trouble to start a thread for Dr.Lester to tell us all about junkDNA and he's not replied once...



Surprise!  Surprise!  He's probably trying to find something written on the subject by D Menton, J Wells, D Gish, or maybe even that  lawyer - Johnson.


 


Posts: 1460 | Posted: 5:51 PM on November 2, 2009 | IP
derwood

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Quote from orion at 5:51 PM on November 2, 2009 :
Quote from derwood at 10:34 AM on October 26, 2009 :
Gee, I go to all this trouble to start a thread for Dr.Lester to tell us all about junkDNA and he's not replied once...



Surprise!  Surprise!  He's probably trying to find something written on the subject by D Menton, J Wells, D Gish, or maybe even that  lawyer - Johnson.





Or his new hero, medical doctor with 30 years of 'studying' evolution under his belt, Dr. Werner....


-------
Lester:

"I said I have a doctorate and a university background in anatomy, physiology, biochemistry, physics, chemistry, pathology etc. ..."
 


Posts: 1646 | Posted: 08:56 AM on November 12, 2009 | IP
    
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