Matheson on introns

| 72 Comments

Steve Matheson, who has been sparring with IDists about their misrepresentations regarding “junk” DNA, has started a series of posts about introns at Quintessence of Dust that’s pitched at the intelligent lay person level and is highly recommended. Part 1 and Part 2 are up so far.

72 Comments

Thanks for the links - I’ve been meaning to check out Matheson’s blog after it came to my attention during this recent “intron debacle”. I have no idea why I hadn’t heard about it before, he seems to know what he’s talking about.

There’s something about “junk DNA” that seems to make it a “crackpot magnet”. Likely the name; the fact that it is, at least in part, imperfectly understood (“I smell a gap!”); and certainly can be obscure, providing opportunities for muddying the waters.

As usual, the controversy over the matter ends up being all out of proportion to its actual level of significance. “No stone left unthrown.”

Another interesting point is the so-called ID “prediction” that there will be no junk DNA. Exactly where do they predict that? Not in anything written by Behe or by Dembski, as far as I know. So where is the prediction made?

The answer seems to be that it is a theological prediction based on the intentions of a Designer, and how an omnipotent Designer would design. They don’t seem to be too eager to acknowledge this, but I haven’t seen any other source for the prediction.

Joe Felsenstein said:

Another interesting point is the so-called ID “prediction” that there will be no junk DNA. Exactly where do they predict that? Not in anything written by Behe or by Dembski, as far as I know. So where is the prediction made?

The answer seems to be that it is a theological prediction based on the intentions of a Designer, and how an omnipotent Designer would design. They don’t seem to be too eager to acknowledge this, but I haven’t seen any other source for the prediction.

I think one reason for the “prediction” is that ID advocates can always claim that any new-found function in junk DNA is evidence for ID, and anyone investigating it is doing ID research. No need for them to even step into the lab themselves.

Yeah, I was thinking that the word “junk DNA” was a particular magnet for creationists because of their “determinism++” mindset: “There can’t be junk in the genome! That would not imply Design!”

Of course, the uncomfortable part of their position is that some noncoding DNA unarguably *IS* junk, like broken genes and viral insertions. I understand viral insertions are surprisingly common, a few percent of the genome IIRC?

But they avoid talking about such things.

Prepare to be boarded and have your liver eaten, Stephen Meyer.

Arg!

The troll light just started flashing … hmm, on checking this one’s MO is very well established, and I would suggest that patience should be accordingly limited.

So-called “junk” DNA attracts them for two reasons -

1) It seems like a potential gap to them - something not fully explained (*although it is much more explained than they realize*). Gaps are a place to temporarily jam “the designer”.

2) It is a strong example of an area in which scientists are active, coming up with explanations for new things and expanding and clarifying current knowledge. A particular favorite game of the denialist is to portray any scientific advance as meaning that “science was previously wrong”.

To a rational, honest person this seems bizarre. Advances are grounded in the work that was done before. If every advance makes everything that went before it “wrong”, then the advance is itself doomed to be rendered “wrong”. This boils down to a “we can never know anything” argument.

To a rigid, brainwashed authoritarian, though, this attitude may make sense. “The rules” should never be changeable, except by the arbitrary act of some authority figure. “The rules” are not internalized, but exist only as the whims of an arbitrary authority figure who must be appeased. The idea of a system of thought that respects all valid contributors, and continuously expands and self-corrects, is an anathema to such minds.

harold said:

To a rational, honest person this seems bizarre. Advances are grounded in the work that was done before. If every advance makes everything that went before it “wrong”, then the advance is itself doomed to be rendered “wrong”. This boils down to a “we can never know anything” argument.

The “Fortean” argument. I am sure that Charles Fort didn’t invent it, but he made it a trademark.

The amusing thing is that if we find out something new and unexpected … then what the current theory is doesn’t matter, it’s still new and unexpected.

Now “throws everything we know for a loop” … well, that happens sometimes, just not often.

LOL! This coming from the guy who comes here to beg for money.

I think you have me mistaken for someone else. Either that, or you’re just pulling whatever out of your tailpipe.

Now “throws everything we know for a loop” … well, that happens sometimes, just not often.

Maybe things such as ether, phlogiston, or epicycles? Those got thrown for that loop. Also early models of atoms got dropped when better ones were invented.

On the other hand, things like Newton’s laws are still in use because they’re close enough at low speeds (relative to light) in flat space (i.e., weak gravity).

But most advances just refine the details, or extend knowledge into areas that weren’t previously explored, rather than rewriting something that was previously firmly established. (Though I don’t know just how firmly established phlogiston was considered to be when the periodic table came along and stepped on it.)

Henry J said:

Maybe things such as ether, phlogiston, or epicycles? Those got thrown for that loop.

I was thinking in terms of epicycles and ether. My favorite is Einstein and the downfall of absolute time, which still throws a lot of people for a loop. Though intriguing even Einstein said it wasn’t a complete game-changer – his “discovery” of the photon (he didn’t call it that) was much more radical, and in fact that’s what he got the Nobel prize for.

Ah, interesting, right? See what REALLY happens to people who successfully challenge the conventional wisdom.

Why the Junk DNA argument is such a big deal for ID creationists is a mystery to me.

Even for a designed system I’d expect some patches and repair after a billion years or so. I mean, my house was designed by an architect and an interior decorator. Originally, I guess, everything was “perfect.” Same for the street designed by an engineer and created with no cracks or potholes. Both are now patched and modified. In the house I’ve got brass taps downstairs and stainless steel upstairs; they don’t match. Outside I’ve got concrete and asphalt and tar, but the road is still drivable.

Same with the genome. Patches here and there, stuff inserted, stuff taken out. It’s a mess but it still works. Seems to me that the ID creationist crowd should embrace Junk DNA and introns as expected.

Don’t get it.

I find the “junk DNA” argument has some parallels to the “creationist information theory” argument. Their ambiguities make them great vehicles for spreading confusion; the fact that neither of them actually back up creationist claims in the slightest is irrelevant to that end.

MrG said:

I think you have me mistaken for someone else. Either that, or you’re just pulling whatever out of your tailpipe.

I’m referring to the Mr.G who constantly links to his “I’m a blogger and if you want to give me money for that I’ll take it” website.

We have a guy in our city park like you who also tells stories in hopes that folks will give him some spare change. But he doesn’t insult us or speak condescendingly like you do.

Oh, how little dogs like to bark.

And you yank somebody’s chain and think they’re going to jump.

Nah. Game over.

MrG said:

Game over.

I’ll take that as an apology for your exceedingly rude behavior earlier.

Doc Bill -

Seems to me that the ID creationist crowd should embrace Junk DNA and introns as expected.

Yes, of course, their arguments are inconsistent.

Disease, suffering, etc, are all the result of the “fall”. Malaria parasites were “designed” and thus must reflect the wrath of the “designer”.

But some fairly harmless nucleotides in the genome that don’t have an obvious sequence-specific function can’t possibly be anything but perfect, functional design.

Look, they don’t care about internal logic, coherence, or honesty. It’s all just “If our kids learn science, they might leave the cult. If your kids can be brainwashed behind your back, they might join the cult. We will say anything or do anything to prevent the former and promote the latter”.

chunkdz said:

MrG said:

Game over.

I’ll take that as an apology for your exceedingly rude behavior earlier.

You mean when MrG assumed you mistook him for someone else in your inane ranting?

I think “Don’t feed the trolls” is written on an ancient scroll somewhere.

This boils down to a “we can never know anything” argument.

Yes, except that it is selectively applied. We can’t know anything that bothers evolution deniers.

You mean when MrG assumed you mistook him for someone else in your inane ranting?

No, fool. I came here to support Steve Matheson’s attack on the Discovery Institute. So I don’t appreciate being called a troll by someone I’ve never spoken to.

chunkdz said:

You mean when MrG assumed you mistook him for someone else in your inane ranting?

No, fool. I came here to support Steve Matheson’s attack on the Discovery Institute.

By eating Stephen Meyer’s liver?

So I don’t appreciate being called a troll by someone I’ve never spoken to.

Then why do you insist on trolling here?

By eating Stephen Meyer’s liver?

He is a ‘political propogandist’ and an ‘enemy of science’. Eating his liver is a metaphor for utterly defeating him in the most humiliating way and laying waste to that ‘wholly corrupt’ ‘intellectual ghetto’ known as the Discovery Institute.

Then why do you insist on trolling here?

Listen fool, I could not care less whether you respond or not. I’d actually prefer that you shut your foul pie-hole and mind your own business. I am here because Captain Matheson is flying the skull and crossbones on a crusade to destroy that ‘intellectual tragedy’ known as the DI, and it’s ‘ignorant’, ‘slothful’ and ‘duplicitous’ proprietor, Stephen Meyer.

Who’s hungry for LIVER!?!?!?

chunkdz said:

By eating Stephen Meyer’s liver?

He is a ‘political propogandist’ and an ‘enemy of science’. Eating his liver is a metaphor for utterly defeating him in the most humiliating way and laying waste to that ‘wholly corrupt’ ‘intellectual ghetto’ known as the Discovery Institute.

This is “civil” to you?

Then why do you insist on trolling here?

Listen fool, I could not care less whether you respond or not. I’d actually prefer that you shut your foul pie-hole and mind your own business. I am here because Captain Matheson is flying the skull and crossbones on a crusade to destroy that ‘intellectual tragedy’ known as the DI, and it’s ‘ignorant’, ‘slothful’ and ‘duplicitous’ proprietor, Stephen Meyer.

If you don’t care if I reply, or if you don’t care about people pointing out how you’re trolling, then why do you routinely vomit up childish invectives when people do point out how you’re trolling?

Who’s hungry for LIVER!?!?!?

If you really do want to murder Stephen Meyer and eat his liver, then why do you insist on calling me a lying, hypocritical bigot when I mention you claiming that?

This is “civil” to you?

Idiot, did you not see the skull and crossbones over at Matheson’s blog? We do not follow your conventional rules of engagement.

If you really do want to murder Stephen Meyer and eat his liver, then why do you insist on calling me a lying, hypocritical bigot when I mention you claiming that?

Fool, did you not see where I told you that this is only a metaphor?

Read before you speak. You will seem slightly less stupid.

If anything, you should take your own advice.

On the other hand, if you did take your own advice, you wouldn’t be here making an asinine idiot of yourself with your childish invectives.

I highly advise that no one feed the Stanton troll.

chunkdz said:

I highly advise that no one feed the Stanton troll.

If I’m a troll, then why is it that everyone holds you in contempt, and why do the admins restrict your IP’s and not mine?

harold said:

The way I understand the observable behavior of someone like Steve P. is that he literally doesn’t have a sense of objective truth the way you and I and Morton do. To the non-Mortons who don’t abandon their false beliefs, no such demon is necessary. They behave as if all of reality is arbitrary and the truth is determined solely by power struggles.

If you go over to Answers in Genesis and watch some of the videos there, you get a pretty good picture of their methods of brain scrambling (e.g., one of the most recent videos “Answers to Difficult Issues”). Every video engages in this brain-scrambling technique.

Ham directs his propaganda primarily at children and adolescents. By the time he gets done with them, it is no longer possible for them to discern the truth or falsity of anything on their own. They have been molded into accepting all their input from sectarian demagogues.

All the ID/creationist sites do this. They mix misinformation and mischaracterizations with demonization and vilification of everyone else who doesn’t hold to their sectarian dogma.

There is plenty of evidence that those who have been immersed in this crap for years no longer have the ability to think on their own; and they hate anyone who can.

Joe Felsenstein said:

Another interesting point is the so-called ID “prediction” that there will be no junk DNA. Exactly where do they predict that? Not in anything written by Behe or by Dembski, as far as I know. So where is the prediction made?

The answer seems to be that it is a theological prediction based on the intentions of a Designer, and how an omnipotent Designer would design. They don’t seem to be too eager to acknowledge this, but I haven’t seen any other source for the prediction.

Joe Felsenstein said:

Another interesting point is the so-called ID “prediction” that there will be no junk DNA. Exactly where do they predict that? Not in anything written by Behe or by Dembski, as far as I know. So where is the prediction made?

The answer seems to be that it is a theological prediction based on the intentions of a Designer, and how an omnipotent Designer would design. They don’t seem to be too eager to acknowledge this, but I haven’t seen any other source for the prediction.

John West informed me that Dembski had made such a prediction in 1998. I will have to look in my archives to see where he made it. I believe it wa sin an interview. Pity that he was almost 3 decades behind the times when he made that ‘prediction.’

slp -

John West informed me that Dembski had made such a prediction in 1998. I will have to look in my archives to see where he made it. I believe it wa sin an interview. Pity that he was almost 3 decades behind the times when he made that ‘prediction.’

Keep in mind the vague, deliberately nontechnical nature of ID “predictions”.

And the word games. The current silliness seems to be - 1) start out with a claim that all cellular DNA must have definitive specific function, 2) get corrected, 3) pretend that the person who corrected you denied any function or activity for all non-gene DNA, 4) declare “victory” when the exact same mainstream scientist who corrected you goes on to study the effects of non-gene DNA.

Steve P.,

You apparently skirted my point (intentional?). I said if cells have the ability to detect, repair, and protect DNA, it would also be logical to assume they also had the ability to discard what DNA could not be repaired. The evolutionary explanation is that genomes store DNA trash accumulated over millions of years, hence the 95/5 junk/good DNA ratio. Which would also mean they had no choice but to store it for lack of ability to deal with unrepairable DNA. This seems a stretch what will all the abilities that cells have.

You are not a scientist; nor am I, that make us perfect discussion partners. You have not responded to me yet, here is another instalment for you to dig into. Please tell me that you know better than me; please tell me how smart you are. It is more likely that you probably won’t or can’t understand what I am trying to say, but anyway:

Your saying ‘if cells have the ability …’ doesn’t necessarily lead to the conclusions you draw. To the contrary, as is the case with so many aspects of nature: The dice rolls the way they do with utter disregard for what ‘logical assumptions’ you make.

Why are you disregarding the extensive research made by well qualified, trained and experienced scientists that spend their lives studying just such subjects and advocate your own, unfounded, unqualified, faith based speculation (or maybe just repeating what you read at creationist sites?) as a superior method of gathering facts?

Is there any reason why the explanation simply is that the cell doesn’t care whether it drags large chunks of non-functional DNA along through its life? Maybe it would cost more to engage in sophisticated maneuvers to get rid of it? To scan the entire genome: this one is ok, that one is useless, do not copy, how do you envisage the mechanics of such elaborate processing of the genome?

Maybe the presence of ‘junk DNA’ is a bonus; a source of raw material for evolution if and when the realities of changing conditions might make evolutionary changes no matter how small, an advantage in the perpetual struggle for survival? Because that, whether you like it or not, is what life is all about.

Because it can’t be any other way. Life’s got to look out for itself, there is in no benevolent designer sitting there with nothing to do except to “intelligently” design modifications to DNA to make a species better equipped to cope with the challenge of survival in an ever changing environment.

We may not ever learn what a designer might or might not do, but all the while we keep learning what nature actually does!

Now please tell us where science is in error, and how you learned that. Scientists would like to know, and so would I. But please, no more of your “If the cell – then” speculation. That is not science; that is applied ignorance.

Game, set, and match, Rolf.

Really late in replying but work has to come first. Crushing load this past week.

Your saying ‘if cells have the ability …’ doesn’t necessarily lead to the conclusions you draw. To the contrary, as is the case with so many aspects of nature: The dice rolls the way they do with utter disregard for what ‘logical assumptions’ you make.

Rolf, can you objectively define ‘roll of the dice’ in biological terms? By the way, how do scientist approach their work if not with logical assumptions???

Why are you disregarding the extensive research made by well qualified, trained and experienced scientists that spend their lives studying just such subjects and advocate your own, unfounded, unqualified, faith based speculation (or maybe just repeating what you read at creationist sites?) as a superior method of gathering facts?

This is an appeal to authority and an argument from labor. A qualified scientist would not proclaim non-coding DNA to be mostly non-functional. Rather that scientist would say that to date with the current research being done and techniques used, about 5% have shown functionality. And that scientist would also say that it is too early to make any conclusive statements about the functionality of the remaining non-coding DNA elements. For people like Moran, Hunt and Matheson to say they are most likely unfunctional is simply speculation and is not based on research results. It is not an objective analysis.

Is there any reason why the explanation simply is that the cell doesn’t care whether it drags large chunks of non-functional DNA along through its life? Maybe it would cost more to engage in sophisticated maneuvers to get rid of it? To scan the entire genome: this one is ok, that one is useless, do not copy, how do you envisage the mechanics of such elaborate processing of the genome?

Why would you contemplate a cell ‘dragging’ large chunks of DNA along through life for millions of years? That is the evolutionary explanation, isn’t it? That junk DNA has build up over millions of years. It seems the cell has a whole lot of closet space.

So at what point does the closet space fill up and junk DNA get put in the hallway or stacked in the dining room? When will overall cell function be impeded under the pressure caused by the build up of so much junk DNA, which it is powerless to discard? What is the evolutionary prediction here?

Harold,

You last post was so much motive mongering.

There is nothing in any post that I have written that could be misconstrued as proselytizing to onlookers. Your trying to stick a Ham or Hovind label on my is at best disengenous or just maybe outright dishonest, seeing how many times you have made the charge in this thread.

FYI, i am in the textile business and make nanofiber fabrics for the sportswear industry. tasks. I simply find the ID/ND debate interesting. I also see so much evolutionary appeals to credulity like ‘hey man, evolution is awesome and we don’t need no God to explain it, either’, which is irritating from a logical point of view.

You have to dig deep to try and avoid the logical conflicts of the evolutionary mindset. The Junk DNA issue is one of these logical conflicts I see.

Steve P. said:

I also see so much evolutionary appeals to credulity like ‘hey man, evolution is awesome and we don’t need no God to explain it, either’, which is irritating from a logical point of view.

This is nothing but pure caricature. It has nothing to do with evolution or science. And it is not very original.

It is like saying your particular textile industry reinvented the sweater.

Yes, Mike, it is a caricature but IMO a valid one and was not intended to be original.

Steve P. said: By the way, how do scientist approach their work if not with logical assumptions???

Why, by using assumptions based on empirical results over 350 years of the Enlightenment.

This is an appeal to authority and an argument from labor.

No, it’s an appeal to qualified authority, which is to say an authority who by dint of study and work over a career knows something about the topic.

A qualified scientist would not proclaim non-coding DNA to be mostly non-functional. Rather that scientist would say that to date with the current research being done and techniques used, about 5% have shown functionality. And that scientist would also say that it is too early to make any conclusive statements about the functionality of the remaining non-coding DNA elements.

We know that much if it is non-coding and non-functional because we can look at the sequences and assess what they might do biochemically, and the answer is “nothing.”

For people like Moran, Hunt and Matheson to say they are most likely unfunctional is simply speculation and is not based on research results. It is not an objective analysis.

It’s an analysis based on research and on a career of studying the phenomena at issue. Again, the appeal is to qualified authority, which though not dispositive is preferable to the ramblings of someone who doesn’t know an intron from an exon.

Why would you contemplate a cell ‘dragging’ large chunks of DNA along through life for millions of years? That is the evolutionary explanation, isn’t it? That junk DNA has build up over millions of years. It seems the cell has a whole lot of closet space.

In fact, cells do have a lot of closet space. And some of them really do appear to be stuffed with junk. How else to explain the pattern shown in T. Ryan Gregor’s Onion test?

So at what point does the closet space fill up and junk DNA get put in the hallway or stacked in the dining room? When will overall cell function be impeded under the pressure caused by the build up of so much junk DNA, which it is powerless to discard? What is the evolutionary prediction here?

When the metabolic cost of reproducing it exceeds the cost of evolving a mechanism to prune it. I can’t specify precisely because I don’t know either cost, but that’s the direction one would take if the question was interesting enough to spend time researching. And if it’s “powerless to discard” it when it becomes a significant metabolic load, why then that species is likely to become extinct. Extinction is a usual and normal fate for species anyway.

Steve P. said:

Is there any reason why the explanation simply is that the cell doesn’t care whether it drags large chunks of non-functional DNA along through its life? Maybe it would cost more to engage in sophisticated maneuvers to get rid of it? To scan the entire genome: this one is ok, that one is useless, do not copy, how do you envisage the mechanics of such elaborate processing of the genome?

Why would you contemplate a cell ‘dragging’ large chunks of DNA along through life for millions of years? That is the evolutionary explanation, isn’t it? That junk DNA has build up over millions of years. It seems the cell has a whole lot of closet space.

So at what point does the closet space fill up and junk DNA get put in the hallway or stacked in the dining room? When will overall cell function be impeded under the pressure caused by the build up of so much junk DNA, which it is powerless to discard? What is the evolutionary prediction here?

Hey, Steve P.,

I posted this about a week ago … perhaps you missed it, being so busy and all. These are serious, sincere questions.

SWT said:

Over at Matheson’s blog I’ve asked the following questions a couple of times … perhaps you’ll be the one to actually answer them:

1) How many design advocates are actually doing research concerning the function of non-coding DNA? What are their key findings? Please point me to their publications on this topic. I’m at a university, so subscription walls are often not a problem for me.

2) How does the answer to 1) compare with the number of functions found by biologists who accept the current mainstream theory to explain biological diversity?

Steve P. said:

The logical question for me is since 1)cells exhibit such a high degree of complexity in general and 2) exhibit skill in detecting and repairing DNA in particular, would not cells also have the capability to eliminate any bits and pieces of DNA that could not be used for any purpose whatsoever?

So why would cells continue to accomodate an ever increasing quantity of useless DNA over millions of years? It makes no logical sense.

IANS, it makes more sense to accept the intuition that because cells demonstrate the intelligent capacity to detect and repaire DNA, they also would have the ability to recognise useless bits of DNA and eliminate them. And if they do not eliminate them, it must be because those bits are functional.

It seems rather pointless to assert that 95% of the genome ‘appears’ to have no function. Why would one call this out? Its as if to say, “Ah, maybe they do and maybe they don’t have function, and you could study it but I wouldn’t waste my time on it because it wont go anywhere”.

If fact, I think studying those genetic elements will in time provide a treasure trove of understanding for a higher order of genome complexity, in constrast to the current thinking that introns and such are ‘most likely’ genetic ‘compost’.

OK, your “intution” tells you that cells have the ability to recognize and eliminate useless bits of DNA, and that DNA that is not eliminated must be functional. You might want to challenge this intuition by asking yourself a couple of questions:

(1) What is the cost of carrying nonfunctional DNA in the genome?

(2) Given that the “elimination” process will probably not be perfect, what would the cost be for a false positive (eliminating “by accident” a DNA segment that was actually functional), and how would that compare with whatever benefit there is to eliminating useless DNA?

(3) How might a cell “recognize” DNA that is useless?

(4) What evidence is there that a mechanism to remove useless DNA is actually in operation?

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This page contains a single entry by Richard B. Hoppe published on July 1, 2010 1:48 AM.

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