Matheson vs. Sternberg

Steve Matheson has been skirmishing with Stephen Meyer during recent weeks and recently he has had a tiff with Richard Sternberg who posted Matheson’s Intron Fairy Tale. Matheson labeled Sternberg's piece a "nasty rebuttal."

Matheson wrote In rage deaf as the sea, hasty as fire at his blog Quintessence of Dust. From that blog entry:

2. Sternberg goes on to list various genomic elements – with various functions that have been established to varying degrees – that can be found in introns. His conclusion can be paraphrased like this:

DNA elements called yadas are sometimes found in introns. Yadas are thought to function in the control of stuff. Therefore introns control stuff.

And here's what this sounds like to me:

Paint cans are sometimes found in piles of rubbish in vacant urban lots (VULs). Paint cans can be used to prop up old cars, or to fight off intruders, or to make music. Therefore VULs are useful in auto repair, home security, and musical composition.

I hope you see that Sternberg's assertion, which is widely made by ID apologists and various creationists, is not so much wrong as it is just silly. And I hope it's a little clearer what I mean when I say that introns aren't known to be functional. Sternberg was wrong to assume that I would share his view of what it means for something to have "function," and he was doubly wrong to think that I would predict that introns don't sometimes – even often – contain elements that serve functional roles. Junkyards, after all, contain lots of stuff that can serve a function.

There is quite a bit of heat being exchanged over a difference having to do with what Matheson means when he says "that introns aren't known to be functional." Before returning to this take a look at Discovery and Analysis of Evolutionarily Conserved Intronic Splicing Regulatory Elements; a study by Gene W. Yeo, Eric L. Van Nostrand and Tiffany Y. Liang appearing in PLOS Genetics. We get a more dispassionate discussion about conserved intronic splicing regulatory elements. The summary:

During RNA splicing, sequences (introns) in a pre-mRNA are excised and discarded, and the remaining sequences (exons) are joined to form the mature RNA. Splicing is regulated not only by the binding of the basic splicing machinery to splice sites located at the exon–intron boundaries, but also by the combined effects of various other splicing factors that bind to a multitude of sequence elements located both in the exons as well as the flanking introns. Instances of alternative splicing, where usage of splice site(s) is incomplete or different between tissues, cell types, or lineages, can be created by the interaction of sequence elements and tissue, cell type, and stage-specific splicing factors. To better understand constitutive and alternative pre-mRNA splicing, the authors describe a comparative genomics approach, using available mammalian genomes, to systematically identify splicing regulatory elements located in the introns proximal to exons. A quarter of the elements were tested experimentally, and most of them altered splicing in human cells. The authors also showed that that the intronic elements are close to tissue-specific alternative exons and are more likely to be located in specific positions in the introns, suggestive of potential regulatory function. These elements are also frequently found in tissue-specific genes, suggesting a coupling between expression and alternative splicing of these genes. Finally, the authors propose a strategy using the elements to identify the binding sites of several splicing factors.

Matheson chose an analogy. Intronic elements connected with regulatory functions sound like this to Matheson:

Paint cans are sometimes found in piles of rubbish in vacant urban lots (VULs). Paint cans can be used to prop up old cars, or to fight off intruders, or to make music. Therefore VULs are useful in auto repair, home security, and musical composition.

Paint cans can be used to prop up old cars, fight off intruders, or make music? Paint cans are analogous to sequence elements? Sounds purposeful if nothing else. Seems to me like this analogy would be better served by including a scaffold firmly anchored and custom fitted in place within the vacant lot. Those on the scaffold have oversight and regulatory responsibilities.

Matheson would probably agree that perceptions are more important than analogies. Matheson wrote this:

The basic story told by DI propagandists and other creationists is that non-coding DNA was ignored for decades, during which it was thought to be completely functionless (due to "Darwinist" ideas), only to be dramatically revealed as centrally important to life.

I don't think the belief was that non-coding DNA was ignored. More like there was an expectation of functionless DNA resulting from an evolutionary process.

This entry was posted on Saturday, June 12th, 2010 at 10:03 pm and is filed under Junk DNA. 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/matheson-vs-sternberg/trackback/

24 Responses to “Matheson vs. Sternberg”

AnaxagorasRules Says:
June 13th, 2010 at 3:33 am
Hi, Bradford,

Those introns are interesting. After reading Sternberg's article, I get the feeling that the introns act something like a control structure in a procedural programming language. Performing a function similar to steering logic. If you took a thousand word procedural (non-objective) program for example, your way of controlling which statements are executed would be determined by the various if, while, for, do-while, switch, and gotos were interspersed in the program. Depending on the control logic on any given execution of the program, you'd have different statements being executed.

Analogously, the nucleoside bases in the DNA strands would be the statements in the program, and the introns (along with whatever else determines which bases get read) would be functioning just as the ifs, switches, and gotos, etc. do in a computer program.

In other words, if I want to take a 100 strand section of DNA, and want to use only every third base, for example, and the only what I'm able to do that is with the introns, then whoa…these introns are vital control structures without which you'd end up with endless logic errors.

Comment by AnaxagorasRules — June 13, 2010 @ 3:33 am

AnaxagorasRules Says:
June 13th, 2010 at 3:38 am
Actually, 'a hundred word program' means 'a program with a thousand executable (non-control) statements'.

Preview is my friend…oh, wait.

Comment by AnaxagorasRules — June 13, 2010 @ 3:38 am

AnaxagorasRules Says:
June 13th, 2010 at 3:39 am
And 'a hundred word program' is really 'a thousand word program' which is really 'a program with a thousand executable (non-control) statements'.

Comment by AnaxagorasRules — June 13, 2010 @ 3:39 am

Bradford Says:
June 13th, 2010 at 7:27 am
Anaxagoras Rules wrote:

After reading Sternberg's article, I get the feeling that the introns act something like a control structure in a procedural programming language. Performing a function similar to steering logic. If you took a thousand word procedural (non-objective) program for example, your way of controlling which statements are executed would be determined by the various if, while, for, do-while, switch, and gotos were interspersed in the program. Depending on the control logic on any given execution of the program, you'd have different statements being executed.

Analogously, the nucleoside bases in the DNA strands would be the statements in the program, and the introns (along with whatever else determines which bases get read) would be functioning just as the ifs, switches, and gotos, etc. do in a computer program.

In other words, if I want to take a 100 strand section of DNA, and want to use only every third base, for example, and the only what I'm able to do that is with the introns, then whoa…these introns are vital control structures without which you'd end up with endless logic errors.

An observation for those who believe that DNA is simply a substance we refer to as a nucleic acid based on its specific properties which include a capacity to store genetic information. Polymer variation allows for adaptive responses to the environment.

Rather DNA is simply a chemical medium through which data can be stored, retrieved and altered to adapt to changing environmental conditions. It is the material evidence of programmed instructions containing control structures and self-correction functions.

Chemical and programming descriptors of DNA both accurately describe its features. The latter descriptor though strongly implies the prior existence of a programmer. The former allows wiggle room within which one can assert the metaphysical *apparent purpose or design but not real* overarching paradigm. Humans can study DNA from either perspective. So as Bilbo wrote in another thread- Game Over. If it is tennis- game, set and match.

Comment by Bradford — June 13, 2010 @ 7:27 am

ID guy Says:
June 13th, 2010 at 9:40 am
Evolutionists do not have any explanation for introns and alternative splicing.

All they can say is that it "just happened" and it must have been good enough to be selected.

However splicing requires knowledge. And molecules in an anti-ID scenario wouldn't have any knowledge.

So they take the "Mayr approach"-> they are comforted by the fact that evolution occurred and they just have some details to figure out…

Comment by ID guy — June 13, 2010 @ 9:40 am

Salvador T. Cordova Says:
June 13th, 2010 at 1:03 pm
Paint cans are sometimes found in piles of rubbish in vacant urban lots (VULs). Paint cans can be used to prop up old cars, or to fight off intruders, or to make music. Therefore VULs are useful in auto repair, home security, and musical composition.

So how would matheson characterize spare tires and backup systems? What metric will he use to argue that it is a functional spare versus fortuitous junk? NONE! He just uses Darwinist ideology rather than serious engineering analysis.

Comment by Salvador T. Cordova — June 13, 2010 @ 1:03 pm

Salvador T. Cordova Says:
June 13th, 2010 at 1:20 pm
Paint cans are sometimes found in piles of rubbish in vacant urban lots (VULs). Paint cans can be used to prop up old cars, or to fight off intruders, or to make music. Therefore VULs are useful in auto repair, home security, and musical composition.

So the space shuttle carries extra navigation systems, food, oxygen, band aids that are never used. By Mathesons ad hoc reasoning, these intelligently designed spares are like junk from VUL's. Matheson's arguments smack of sophistry, not serious engineering engineering analysis.

Comment by Salvador T. Cordova — June 13, 2010 @ 1:20 pm

AnaxagorasRules Says:
June 13th, 2010 at 2:30 pm
Hi, Bradford,

Chemical and programming descriptors of DNA both accurately describe its features. The latter descriptor though strongly implies the prior existence of a programmer. The former allows wiggle room within which one can assert the metaphysical *apparent purpose or design but not real* overarching paradigm. Humans can study DNA from either perspective.

And some people can analogize the nucleus to a junk-filled vacant lot. How disgustingly crass.

Comment by AnaxagorasRules — June 13, 2010 @ 2:30 pm

Bradford Says:
June 13th, 2010 at 2:34 pm
Anaxagoras Rules:

And some people can analogize the nucleus to a junk-filled vacant lot. How disgustingly crass.

I expect more from an aficionado of Shakespeare.

Comment by Bradford — June 13, 2010 @ 2:34 pm

AnaxagorasRules Says:
June 13th, 2010 at 3:31 pm
After reading Matheson's rationale for declaring introns to be mostly nonfunctional…that being that functions haven't been discovered for the large majority of them yet, I nominate him to be the poster boy to represent what's wrong with a Darwinian philosophy applied to the cell. What an ignorant jerk, despite his education.

Comment by AnaxagorasRules — June 13, 2010 @ 3:31 pm

Salvador T. Cordova Says:
June 13th, 2010 at 8:47 pm
VULs are useful in auto repair, home security, and musical composition.

Last I remember, the ability to recycle junk to make something useful requires some innovation and resourcefulness, or in other words: INTELLIGENCE!

So if Matheson is saying that junk is being used to an innovative end, it doesn't help his argument in the least!!!

Comment by Salvador T. Cordova — June 13, 2010 @ 8:47 pm

Salvador T. Cordova Says:
June 15th, 2010 at 3:36 am
Wells effectively puts the specter of Matheson out its misery:

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

Hahaha!

Comment by Salvador T. Cordova — June 15, 2010 @ 3:36 am

Salvador T. Cordova Says:
June 15th, 2010 at 3:58 am
Larry Moran needs to correct the spelling of his last name:

And Moran’s guess that only about 5% of human genes undergo alternative splicing is flatly contradicted by 2008 articles in Nature and Nature Genetics, as well as the 2010 Nature article cited by Sternberg. In lieu of factual support for his claim, Moran ridiculed Sternberg for giving “no indication that he understands the controversy” and basing “his entire fairy tale on a value [i.e., 95%] that has been pretty much discredited.”

Comment by Salvador T. Cordova — June 15, 2010 @ 3:58 am

Bradford Says:
June 15th, 2010 at 7:06 am
It's the tactics of personal destruction in view Salvador. Larry Moran would be nicer to a child molester. Stephen Meyer left the door open to a thought odious to that mindset. Carelessness is the bedfellow of their arrogance.

Comment by Bradford — June 15, 2010 @ 7:06 am

Salvador T. Cordova Says:
June 15th, 2010 at 11:15 am
I'm afraid Larry got his ideas from Art, and Art got his ideas by misreading the literature.

I pointed out Art's error here:

Art mistake 1

and

Art mistake 2

I'm giving Art the chance to defend himself, but I think he's made a mistake. To his credit, Art's been much more civil than Larry.

Comment by Salvador T. Cordova — June 15, 2010 @ 11:15 am

Salvador T. Cordova Says:
June 15th, 2010 at 11:18 am
It's the tactics of personal destruction in view Salvador. Larry Moran would be nicer to a child molester. Stephen Meyer left the door open to a thought odious to that mindset. Carelessness is the bedfellow of their arrogance.

Larry's looking kinda senile these days. I've read some of his blog, he seems to have reading comprehension issues. Wells pretty much slammed Moran to the floor.

Comment by Salvador T. Cordova — June 15, 2010 @ 11:18 am

Guts Says:
June 15th, 2010 at 11:36 am
I would be cautious about making general statistics on the number of AS events occuring in a cell out of those numbers since they are limited by the depth of sequencing. I would definitely expect more AS events to occur.

Comment by Guts — June 15, 2010 @ 11:36 am

Salvador T. Cordova Says:
June 15th, 2010 at 11:48 am
Guts,

I think Art made a serious mis-reading of the literature. I could be wrong, but I don't think he can make those claims.

The mistake is like saying:

6% of cars have GPS built in, therefore 6% of cars with built-in GPS have a GPS receiver!

the correct characterization is

6% of cars have GPS built in, but 100% of cars with built-in GPS have a GPS receiver!

Sal

Comment by Salvador T. Cordova — June 15, 2010 @ 11:48 am

Salvador T. Cordova Says:
June 15th, 2010 at 1:05 pm
I posted this at UD:

Spare Tires and Operating Systems:

I should point out there are legitimate and illigitimate ways of characterizing functions.

It would be illegitimate to cherry pick all the days where spare tires on cars are not used. It would be illegitimate to say, "the spare tire wasn't used on July 19, 2001, therefore the spare tire serves no function".

In similar fashion, it would be illigitimate to say certain features of an operating system (like Windows 7) aren't functional merely because we find computer users who don't use all the features of the operating system!

We certainly might find introns in some cells that are not used, but it would be deeply improper to generalize the behavior of introns in one cell type to all cell types. In fact Mattick argues introns are used differently in each cell type.

If indeed the cell uses operating systems like modern computers, and if cells have backup systems like spare tires, we would actually expect cells to have functional capabilities that are not always utilized. The lack of utilization 100% of the time is not evidence against function anymore than the lack of use of a spare tire or unused feature of an operating system is evidence against its function.

Comment by Salvador T. Cordova — June 15, 2010 @ 1:05 pm

Salvador T. Cordova Says:
June 15th, 2010 at 1:14 pm
Also:

The reason I mentioned spare tires and operating systems is that Art is referencing the behavior of a single cell type to make his case.

There are, according to Mattick,
10^12 or 100,000,000,000 positionally differentiated cell types. I’d say even if Art makes a case for one cell type, (and I’m still disputing he got the account correct), he is making an awfully hasty generalization given we have, according to mattick 100,000,000,000 positionally differentiated cell types.

It would illegitimate to say that because you found a computer user that only uses 5% of Windows 7, therefore 95% of Windows 7 is non-functional!

I claim Art’s citation of from Sultan’s paper is equally flawed. He is more than welcome to contest my characterization of what he said.

Thanks in advance to Art for his response.

Comment by Salvador T. Cordova — June 15, 2010 @ 1:14 pm

Salvador T. Cordova Says:
June 15th, 2010 at 3:09 pm
10^12 or 100,000,000,000

There is a typo, it should read

10^12 or 1,000,000,000,000

Also at UD:

There is also a possible quivocation he way Art is arguing against Sternbergs claim:

At least ninety percent of gene transcripts undergo alternative splicing, and there are at least 190,000 introns in the human genome.

A charitable reading is 90% of the KINDS of transcripts existing emerged from alternative splicing.

How can this be? a manufacturing analogy is inorder.

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 kinds of cars went through alternative splicing (so to speak).

Hopefully the clarifies further the mis-use by Art of Sultan’s paper.

Comment by Salvador T. Cordova — June 15, 2010 @ 3:09 pm

Salvador T. Cordova Says:
June 15th, 2010 at 3:38 pm
Wells points out:

scientists reported that the majority of human genes generate almost eight different messenger RNAs.

Worst case 50% of genes have 8 different mRNA's. That means on worst case, on average each gene has 4 different mRNA, which implies, worst case 3 out of 4 alternative splices, or 75%.

Yet ole senile Moran is sticking to his 5% number.

Comment by Salvador T. Cordova — June 15, 2010 @ 3:38 pm

Salvador T. Cordova Says:
June 16th, 2010 at 12:10 pm
Here's a howler regarding Senile Moran. Wells observes:

And Moran’s guess that only about 5% of human genes undergo alternative splicing is flatly contradicted by 2008 articles in Nature and Nature Genetics, as well as the 2010 Nature article cited by Sternberg. In lieu of factual support for his claim, Moran ridiculed Sternberg for giving “no indication that he understands the controversy” and basing “his entire fairy tale on a value [i.e., 95%] that has been pretty much discredited.”

Yet Moran provided no justification for his ex cathedra pronouncement that the 95% figure has been discredited. He simply brushed aside the 2008 and 2010 articles in Nature and Nature Genetics and their eighteen co-authors—nine of whom listed their affiliation as Moran’s own institution, the University of Toronto.

Comment by Salvador T. Cordova — June 16, 2010 @ 12:10 pm

In Defense of Hidden Objectives - Telic Thoughts Says:
June 17th, 2010 at 12:06 am
[...] 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 [...]

Pingback by In Defense of Hidden Objectives - Telic Thoughts — June 17, 2010 @ 12:06 am

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Matheson vs. Sternberg

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