Matheson on introns

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.

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.

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.

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

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.

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.

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

chunkdz said:

MrG said: Game over.

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

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.

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

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.

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

By eating Stephen Meyer’s liver?

Then why do you insist on trolling here?

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.

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!?!?!?

This is “civil” to you?

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?

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.

Matheson makes an excellent point that many introns that demonstrate functionality still possess long stretches of non-functional code. Wouldn't you agree, Mr.G?

Actually, Matheson's points in his latest post are that introns take up tremendous portions of the gene and do not contribute coding for the primary gene-product, and that intron sizes, but not number, vary from species to species, in addition to the facts that very few introns appear to have any functions, and of those few introns that have functions, i.e., coding for microRNA, the vast majority has no apparent function.

The folks who are engaging in the side feud, please take to AtBC. Don't pollute this thread with your sniping, please.

I agree completely, RBH. I think Stanton should leave if he can't control himself.

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.

Intelligent Designer said: It's nice that you guys can make our arguments for us and then refute them. I've never predicted that there is no junk DNA. One would expect some as a result of entropy.

RBH said: The folks who are engaging in the side feud, please take to AtBC. Don't pollute this thread with your sniping, please.

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'.

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’.

The logical question for me

Steve P. said: 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'.

Intelligent Designer said: I've never predicted that there is no junk DNA. One would expect some as a result of entropy.

Steve P. said: ... 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.

SWT said: So, which is the prediction from ID?

Intelligent Designer -

Who is the designer? What tests can I do to rule out other designers? What did the designer do, and when? Please give me a sufficiently detailed idea for an experiment that I can do to differentiate precise, specific actions of the designer from natural events.

Steve P. -

Intelligent Designer is not a Christian and has condemned the doctrine of eternal damnation in other threads. How do you feel about that? Is he still your buddy because he denies the theory of evolution?

Albatrossity said:

SWT said: So, which is the prediction from ID?

The prediction from ID is that genomes have been degrading ever since the dezinner slapped them together - aka genetic entropy. Oh, wait. That was the other prediction. Never mind...

SWT said:

Intelligent Designer said: I've never predicted that there is no junk DNA. One would expect some as a result of entropy.

Take it up with Steve P.:

Steve P. said: ... 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.

So, which is the prediction from ID?

harold, please remember that it is not Randy Stimpson's and Steve P's responsibility to explain how or why Intelligent Design Theory is better than Evolutionary Biology, who the Intelligent Designer really is, or how or when the Intelligent Designer does anything, or even point out the flaws of a fellow evolution-denier's "arguments"

It is their sole responsibility to repeat that "evolution doesn't work" over and over again, while making appeals to faith, ignorance and incredulity.

Kevin B.Please feed “chunkdz” to the billy goats!

phantomreader42 said: ID simultaneously predicts that every single base pair of every single gene is junk (as DNA doesn't need to actually do anything since GOD THE DESIGNER makes everything happen by magic), AND that there is no junk DNA whatsoever (since GOD THE DESIGNER wouldn't create something useless), AND every percentage in between. ID also predicts that junk DNA both has no function whatsoever AND has countless mutually exclusive functions.

eric said:

phantomreader42 said: ID simultaneously predicts that every single base pair of every single gene is junk (as DNA doesn't need to actually do anything since GOD THE DESIGNER makes everything happen by magic), AND that there is no junk DNA whatsoever (since GOD THE DESIGNER wouldn't create something useless), AND every percentage in between. ID also predicts that junk DNA both has no function whatsoever AND has countless mutually exclusive functions.

Perhaps we should start calling this the 'Spartacus defense.' Scientists ask IDers to put forward a testable ID hypothesis; in response, IDers propose a thousand different ideas as a means of preventing ID from being tested.

There once was a Man from Nantucket,

who said, "The Designer has muffed it."

"Consider Anatomy,

I just don't make sense to me."

Having fun next to sewage don't cut it!

Steve P. is a predictable creationist who will not be convinced by evidence and rational thought. However, for the sake of third party readers, I will point out his errors in reasoning. A number of them are quite instructive. We should bear in mind that Steve P. probably does not spontaneously think in the way his arguments suggest, on a day to day basis. Rather, he probably perceives it to be in the interest of his authoritarian, politically-involved cult to “say anything that attacks evolution”.

“Complexity” is used here an undefined magic word. It is not relevant to the discussion, or even to his own arguments. Of course, I welcome him to prove me wrong by employing an objective definition and showing how it is relevant.

Cells have DNA repair mechanisms. They do not “exhibit skills”. Below, Steve P. continues to anthropomorphize and attribute to individual cells, characteristics of integrated neuromuscular systems.

We could mistake this fetish for individual cells for a bizarre spiritual belief, as it is obviously not part of traditional Christianity. But we must remember that Steve P. is probably merely “saying anything to attack evolution”. He has been taught that repetition the words “intelligent” and “complexity” is part of the propaganda approach

DNA repair mechanisms are not perfect. Accumulation of non-coding DNA is not a major target of many of the DNA repair mechanisms, as well. “Logical problem” solved.

Steve P. doesn’t have the inclination, or perhaps ability, to learn anything real about either DNA repair or non-coding DNA, yet falsely implies expertise.

For those who are confused, let me remind you that Steve P. probably does not have the concept of “honesty” that we do. His task is to “argue against evolution” and “advocate for intelligent design”. His technique includes meaningless repetition of the words “intelligent” and “complexity”.

It certainly doesn’t matter what an dishonest ignoramus thinks.

Steve P. said: On the contrary, complexity is central to the argument. By the way, I don't have a rigourous definition of complexity so you can discard that lame 'dishonest' label you like to paste on IDists.

If you actually understood the mechanisms for DNA repair, it would occur to you Steve that there is in fact no logic in assuming that somehow the cells have a magic useful DNA detector.

Steve P. said: Is the cell's repair capability learned? If so, they have a skill. ...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. ...cells would have no choice but to store DNA trash for lack of ability to deal with unrepairable DNA. This seems a stretch...

Steve P. said: 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.

“Complexity” is used here an undefined magic word. It is not relevant to the discussion, or even to his own arguments. Of course, I welcome him to prove me wrong by employing an objective definition and showing how it is relevant.

On the contrary, complexity is central to the argument. By the way, I don’t have a rigourous definition of complexity

Cells have DNA repair mechanisms. They do not “exhibit skills”. Below, Steve P. continues to anthropomorphize and attribute to individual cells, characteristics of integrated neuromuscular systems.

The definition of skill from merrium-webster online; definition 2b: dexterity or coordination especially in the execution of a learned task. Is the cell’s repair capability learned? Do cells coordinate their molecular activity during DNA repair? If so, they have a skill.

DNA repair mechanisms are not perfect. Accumulation of non-coding DNA is not a major target of many of the DNA repair mechanisms, as well. “Logical problem” solved.

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.

harold said: In both cases, the person may be delusional at the conscious level.

MrG -

Maybe, but Morton's Demon was described by Morton, who eventually abandoned false YEC beliefs. http://www.answersincreation.org/mortond.htm

I don't exactly think that the likes of Steve P. are conscious frauds the way a typical kid trying to use a fake ID to buy beer is a conscious fraud.

It's more as if the kid is literally convinced that "age" is determined by tricking or threatening others into accepting arbitrary numbers. The idea that two people can agree to measure the passage of time by reference to the rotation and revolution of the earth, or to measurable atomic decay, is ludicrous to him. Life is about deciding the way you want things to be and demanding that others submit to that demand.

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.

Steve P. is totally committed to saying anything, however irrational or unsubstantiated, to contradict the theory of evolution or advance his (hidden)agenda one tiny step at a time. In this way he is typical of creationists. Morton was highly atypical, as proven by his abandonment of YEC rather early in life.

No argument or accumulation can "convince" Steve P. The idea of coming to a consensus through mutual objective examination of the evidence is alien to him.

Please note that I am talking about observable behavior here. We are talking about people who will repeat back disproved arguments, admit that they can't define a word yet claim it is central to their argument, etc. Logic and evidence play no role. Force of will is all they care about. I won't stop repeating it, so it must be true.

There are Mortons and potential Mortons out there, and that's why I bother to engage with the hopeless nihilistic authoritarians.

Of course, reality always catches up. If the creationists of the world succeed in setting up a hard core right wing theocracy and stamping out human understanding of evolution, life will still evolve around them.

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.

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.

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.’

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.

Game, set, and match, Rolf.

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?

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.

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???

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.

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?

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?

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'.