It's time to talk about introns and function, so at least the ID people and I can agree on what we're disagreeing about. First, though, a little housecleaning.
When confronting the avalanche of misinformation on so-called "junk DNA" from intelligent design creationists, it can be hard to know where to start. In a previous series, I addressed many of the falsehoods that are employed by these folks, but the basic outline of the problem is easy to lose in the fog of confusion that ID advocates and other creationists purposefully generate around the issue. You can learn all you need to know by reading the previous series, and by reading the extensive work of Ryan Gregory. But here's a brief re-introduction.
I would say there are two main components to the "junk DNA" misinformation effort.
1. ID advocates and other creationists claim that "Darwinists" assumed that non-coding DNA was functionless, right from the moment it was discovered. And so scientists failed to study non-coding DNA, leading to a vast knowledge gap that has cost human lives.
2. ID advocates and other creationists claim that "Darwinists" still assume that all non-coding DNA is functionless.
(Now, note that I won't even deal with the counter-claim, the only one that should matter for someone truly trying to establish an explanatory role for design: that genomic elements show properties that one would expect in a designed system. Plenty of ID advocates say that genomes look efficient and brilliant and excellent, but they're not so good at explaining exactly how genomic structures display the relevant characteristics. That's for another time.)
Back to those two components. They're both falsehoods.
Let's look at the first point. Read Ryan Gregory on the history of scientific thought on the subject: biologists did not make that assumption, indeed there was diversity of opinion on the amount of function in non-coding DNA from day one. Moreover, Darwinists were and still are most likely to postulate function for most genomic elements, since they were and are more likely to ascribe biological features to adaptation. And worse, the claim that non-coding DNA was ignored for decades is demonstrably false. I'm afraid it doesn't matter that some science writers (and one confused biologist) claim otherwise. There have surely been changes in attitudes toward genomic structures of various kinds as genomes have become so much better known. But the claim that biologists always assumed that all non-coding DNA is junk is just flat wrong, and you can read the bloody scientific literature yourself to see why.
And now the second point. Every time a cool new microRNA turns up in an intron, or a retroviral sequence is found to comprise a structural gene, or a pseudogene is shown to influence gene expression, ID propagandists go bananas as though they've just overturned evolutionary theory. Why? Because they seem to actually believe that "Darwinists" (by this they mean people who accept evolutionary theory in just about any of its forms) still think that non-coding DNA is all junk. The reality of current controversies in genomic structure and evolution couldn't be more different. Some hard-core adaptationists (the truest "Darwinists") share ID's commitment to the notion that genomes should contain very little non-functional debris, and you can learn a lot about the mendacity of ID mouthpieces by reading the disagreements between Larry Moran and his Darwinist detractors.
So, let's learn a little about introns. It should be fun. But don't fall for the misinformation from the propaganda network. In fact, think of "junk DNA" as an integrity dipstick. If you see those falsehoods on the dipstick, you're probably reading propaganda or uninformed nonsense. Caveat lector.
55 comments:
I'm sure it were ID advocates and creationists who came up with the term "junk"-DNA...
Great post Steve. Looking forward to the series.
I've always enjoyed the irony that the most extreme Darwinian position on "junk" DNA is indistinguishable from .... the ID position.
I have to laugh when I read about the ID or YEC-based "predictions" that junk DNA will be found to be functional. Yu ask when these predictions are made, and if you get an answer at all, you are told something like 'Bill Dembski predicted this in 1998', and when you provide the person making this claim with, say, a half dozen citations dating back to the 1970s indicating that 'Darwinists' were actually looking into and discovering functions for decades before these amazing' predictions' were made, you are told that such papers were published IN SPITE OF the prevailing Darwinist suppression of truth, and that it was not 'mainstream.'
They just cannot let a good lie go...
Looking forward reading the usual pseudonymous experts on the real science behind Introns.
;)
"Although very catchy, the term "junk DNA" repelled mainstream researchers from studying noncoding genetic material for many years."
Scientific American, Feb 2007
Steve, even if the above is false as you say, it is nevertheless disingenuous for you to attribute this mindset solely to your intellectual enemies. SciAm in 2007 can hardly be called ID or creationist publication.
But what the hell - we're flying the Jolly Roger here! LET'S SLIT SOME THROATS AND EAT SOME LIVERS!!
Matheson: "So you see, I didn't attribute the mindset solely to my "intellectual enemies.""
Umm, you linked to one "confused" creationist and one "extreme[ly] biased" journalist. Sounds like intellectual enemies to me.
My quote, on the other hand, was from Wojciech Makalowski from Penn State. He's not merely a "science writer" - he's a respected scientific researcher in the relevant fields - I'm sure you've read some of his recent papers on introns and such for your upcoming treatise on the subject. He seems pretty knowledgable, [your "lame" label notwithstanding].
Don't get me wrong, Steve, I am completely in support of your Culture War. Just try not to give the fundies too much ammunition by being disingenuous.
Matheson: "Find some new friends."
I don't want friends, I want to see you SLIT THROATS AND EAT LIVERS!! I want blood and guts and gore and veins in your teeth!
But be honest about it.
First, let's read the entire paragraph from Sci Am.:
"Although very catchy, the term "junk DNA" repelled mainstream researchers from studying noncoding genetic material for many years. After all, who would like to dig through genomic garbage? Thankfully, though, there are some clochards who, at the risk of being ridiculed, explore unpopular territories. And it is because of them that in the early 1990s, the view of junk DNA, especially repetitive elements, began to change. In fact, more and more biologists now regard repetitive elements as genomic treasures. It appears that these transposable elements are not useless DNA. Instead, they interact with the surrounding genomic environment and increase the ability of the organism to evolve by serving as hot spots for genetic recombination and by providing new and important signals for regulating gene expression."
Second, this was from a column in Scientific American called "Ask the Experts." Sort of like Ask Andy or Dear Abby.
Third, Scientific American is a popular science monthly, sort of like Time Magazine for science; popular science written by invited scientists and engineers at an 8th-grade level. No, it's not a creationist publication but it is edited, not reviewed, and pitched as an overview of current science.
If you want to hang your argument on a quote from Sci Am and that's all you've got, you are well and truly hung.
. . . read the bloody scientific literature yourself . . .
I think I've spotted a flaw in your attempt to educate the Intelligent Design Creationists
chunkdz, point taken. I'll make that "two confused biologists."
You've got to work on this Culture War stuff, Steve. Calling John Mattick "confused" is like calling Lewis and Clark "confused". He's just blazing a trail on a hunch and finding a lot of cool things along the way. Think of a better polemic label.
Looking forward to learning about introns. AND EATING SOME LIVERS!
Hi Steve,
I don't get all worked up about the debate over how much non-coding DNA is functional and how much isn't, because:
1) Both Mike Gene and Michael Behe allow for much randomness in evolution, which,it seems to me, would at least allow for the possibility of much non-functionality.
2) Mike Gene has shown how much of the non-coding DNA would fit into his front-loaded evolution hypothesis.
3) The question of functionless DNA does not address Behe's arguments for dessign.
But I see where the question of functionless DNA would be a problem for YECs. I'm not a YEC, so I'll just read a long as you explain how most DNA is functionless, and then I'll wait to see if biologists uncover more function or not. But, hey, knock yourself out.
I don't know if Mattick has changed his tune, but his past assertions about the contributions that small and non-coding RNAs makes to bacterial genome function are way past confused - they are just plain wrong.
Anyone who takes Mattick's well-publicized claims without very large grains of salt is going to be seriously mislead when it comes to small RNAs in biology, or the matter of transcription in eukaryotic genomes. He's wrong on these two issues, fundamentally so.
(I haven't kept up with Mattick's work and have no idea if he is revising his ideas. But, as many of the talks and posters at the RNA 2010 Meeting reveal, such revisions are needed.)
Bilbo, you refer to "Mike Gene" which is a pseudonym for a person with no scientific qualifications whatsoever, and Mike Behe who has done no research on "junk DNA" whatsoever.
I don't see your point. "Front loading" is no more a hypothesis than floating mountain islands as proposed by James Cameron.
Seriously, Bilbo, if you want to propose comedy then please do better!
Hi Bill,
First, how do you know what Mike Gene's qualifications are? Second, are you able to state what his hypothesis is? Third, the question of how much research Behe has done on "junk DNA" is irrelevant. He admits that random mutations have been a big part of evolution, which is part of the standard neo-Darwinian explanation of why we have "junk DNA." My point is that even if 98.5% of DNA was junk, this would be irrelevant to either Mike Gene's or Behe's positions. If you think that's comedy, I'm sorry it didn't make you laugh. I always find your comments rather amusing, How are things in your part of the gulf?
(I can't make the "reply" function work.)
First, MG told me (and everybody) that he has no scientific training, experience nor background; he's only "interested." The difference between MG and James Cameron is that JC had an amusing story to tell. MG, not so much. Yes, I know what "front loading" is and it has no basis in reality, no more than floating mountains or winged horses. Fun to contemplate as fiction. Don't you realize that MG is just jacking with you?
MG and Behe don't have scientific positions. Isaac Asimov was a scientist and a science fiction writer, but who would call anything he wrote an hypothesis? That's the common thread that runs through all creationists; they have no appreciation of literature (ironic, eh?) and absolutely no sense of humor. Seriously, name a funny creationist. I mean funny ha-ha, not funny *cough*Luskin*cough* peculiar.
Finally, even if 200% of DNA was junk it would be irrelevant to MG and Behe's positions because they don't have positions, just poses like Lady Gaga without talent.
It's summer here in the gulf. Warm, moist Gulf air as they say. My distant cousin, an avocado, sprouted and unfolded three leaves.
Hi Bill,
(I still can't get the reply thing to work.) I think you misunderstood Mike about his qualifications. We've wondered for years what his qualifications are, but he won't say. So I rely upon Arthur Hunt. He's been Mike's thorn-in-the-side for as long as I can remember. If Art thinks he has a good hand, he'll play it. If he thinks Mike has a point, he won't admit it, but he goes suddenly silent. He makes a bad poker player, but a good indicator of whether Mike is onto something. So based on Art's non-reactions and from what I can figure out on my own, I would say that Mike has a good case for front-loaded evolution. But maybe you see it differently. But you'll need to provide some good arguments or evidence to the contrary.
chunkdz:
"My quote, on the other hand, was from Wojciech Makalowski from Penn State."
You've got a quote! Well, a quote trumps any data in your mind, right?
Hi Arthur,
You guys really aren't getting this.
Of COURSE Mattick is "wrong". How could he NOT be. But we are flying the freakin' JOLLY ROGER here! That means we take no prisoners.
Try something like this:
"The most disturbingly creepy thing about John Mattick is the way his wrongness gives aid and comfort to the IDiots. I can only attribute his wrongness to some combination of ignorance, sloth, and duplicity."
That's how you do it Arthur. It's also much more devastating if you say it while wearing a crocoduck T-shirt.
No, moron. That's why I circumspectly told Steve "even if the above [Makalowski quote] is false".
The point was that Makalowski, right or wrong, is probably not an intellectual enemy, and can probably provide a lot of good information on introns. Information that we can then use to cut out the still beating hearts of our REAL intellectual enemies and make them watch as we eat them. Capische?
"The point was that Makalowski, right or wrong, is probably not an intellectual enemy, and can probably provide a lot of good information on introns."
So let's talk about his DATA, not what he says.
Hmm…should I add "moron" too? Nah, I won't. Your desperate need to put quotes above data says it all.
That's the point. Capische?
(If you want the reply thing to work, Bilbo, I'd suggest you buy a MacBook Pro rather than using the coin operated Internet kiosk at QuikTrip.)
So, you say that MG has a "good case" based on what someone DOESN'T say and you incredible talent for "figuring out." What's next, asking me to rebut MG's fantasy? Oh, lookie, I guessed right! I should be picking lottery ticket numbers!
Tell me, my little hobbit, why is it you gleefully live in the MG Matrix rather than ride to Zion and party like it's 3999? What is it about Magick that so appeals to you? Impressed by that quarter you got from the Tooth Fairy? Me, too, but, alas.
JohnZ: "So let's talk about his DATA, not what he says."
The quote IS data, fool!
Specifically, data that shows that at least one respectable scientist says that non-coding DNA was ignored for some time.
Now, maybe Makalowski is really an IDiot in which case he will be lashed and beheaded and have his bloody skull framed and displayed in the title banner of Steve's blog. But that remains to be seen.
Quotes are not data. You fool yourself, fool.
"My dog has fleas" is a quote.
A chart showing flea count per square inch of dog per month is data.
Try education. You'd be amazed what you learn.
Dumbass Doc Bill: "Quotes are not data. You fool yourself, fool."
If the question is "do reputable scientists say non-coding DNA was ignored?"
then data would probably include a quote from a reputable scientist saying that NON-CODING DNA WAS IGNORED.
Stick to counting fleas, dumbass. Staring at a dog's butt sounds like the perfect job for you.
Hi Bill,
The kiosk is a lot cheaper. You don't have to try to refute Mike, if you don't want to, but don't expect me to just take your word for it that front-loaded evolution has no basis in reality. Mike has been producing results for far too many years to be brushed off that easily.
As for magic, every time something happens there is magic.
But what I'm really curious about, at the moment, is how long before Chunk gets banned here. I would have banned him at TT a long time ago.
Do you think Chunkers was "fishing" for an insult calling me a Dum Bass? Sounds like carping from a minnow to me. I'd rise to the bait but I'm nearly out of puns.
As for Gene, he has no results. Whatever you're smoking I'd like two, please. Gene has a self-published "popular" book that ranks about 2 on the Behe Mediocrity Scale. Behe has "The Edge," MG has "Full Monty Loading," Dembski has "The Filter," Meyer has "The Signature" and my dog has "The Fleas."
Sorry, Bils, but you're going to have to lay off the tripe if you intend to squeeze into your cheerleading costume.
You win the punic wars, Bill. But I doubt you have much familiarity with Mike's work.
Steve wrote: " so at least the ID people and I can agree on what we're disagreeing about"
I agree that Dr. Matheson made this statement:
"Let’s say that a hundred introns in the human genome are known to have “important functional roles.” Oh fine, let’s make it a thousand. Well, guys, that leaves at least 189,000 introns without function,"
So if we don't know something has function, according to your Mathesonian logic, it doesn't have one. That's a howler (howler is a a phrase you have used in this blog to describe the writings of ID proponents).
I'll agree you made that silly statement on your blog. You shouldn't resort to "argumentum ad ignorantiam" to defend your position. It's a logical fallacy.
If you're arguing "we don't know something has function, therefore it has none, and therefore further search for function shouldn't be explored" -- that's silly and plain bad science.
If you're not arguing that, but instead argue that we merely don't know whether introns have function, then Meyers claim and prediction that introns have function is not so ludicrous (which is how you characterized his claim).
In either case, you're assertions are self-contradictory. So if you then give blessing for the search for predicted functuon in introns, you've essentially retracted the characterization that Meyer's claim is ludicrous.
By the way, Dr. Matheson, it's my understanding Clive Hayden UD has invited you back to the discussion at UD.
If you decline the invitation, I'm happy to link to our exchanges here.
Bilbo, your liver gets eaten first.
Let's agree that Dr. Matheson characterized this claim by Dr. Meyer as ludicrous:
" Although these introns were once thought to be nonfunctional "junk DNA," they are now known to play many important functional roles in the cell."
Now, applying Darwinist "logic", we say regions of DNA across species that are identical are called "conserved". Darwinist "logic" states that if they are "conserved" it is because they confer selective advantage, and if they confer selective advantage, they must be functional.
And that is exactly the conclusion of Mondal,Rasmussen, Pandey, Isaksson and Kandur. They argue, using Darwinist "logic":
"Noncoding RNA (ncRNA) constitutes a significant portion of the mammalian transcriptome. Emerging evidence suggests that it regulates gene expression in cis or trans by modulating the chromatin structure. ..Our data suggest that ncRNA is an integral component of chromatin and that it may regulate various biological functions through fine-tuning of the chromatin architecture."
So even on the grounds of Darwinist reasoning, Meyer's claim that we know introns have function is supported by evolutionists. His statement therefore is hardly ludicrous.
But if you insist in saying Dr. Meyer's claim is ludicrous, you'll also have to assert the work of your Darwinists colleagues who swear by the idea:
"conserved regions" = "functional" DNA
is also ludicrous. :-) Are your Darwinist colleagues like Mondal right or wrong? :-)
If you say they are right, then you've effectively conceded Dr. Meyer is right. If you say they are wrong, then you'll have to explain why we should reject comparative genomics and the search for "conserved" regions using Darwinist reasoning for "conserved" regions. Either outcome will not reflect well on the positions that you've dogmatically asserted.
Eh, if anyone has any doubt as to what an ad hom argument is, read all of the posts written by "Doc Bill". Doc Bill, let me know when you decide to actually get specific as to Mike Gene's intron hypothesis.
Hi Chunk,
I'm pretty sure Steve isn't going to eat anyone's liver. I'm just curious if he thinks people who call people 'moron" or "dumbass" on his blog should be tolerated.
No, the question isn't whether or not reputable scientists say that non-coding DNA was ignored. The questions is, was non-coding DNA actually ignored? The fact that we're having this discussion, and that the discussion has been ongoing since Ohno's 1972 presentation, is evidence that non-coding DNA has not been ignored.
Hi Bilbo,
Perhaps you don't realize who it is that Steve is fighting. These are 'ignorant', 'slothful', 'duplicitous', 'ludicrous', 'stupid', 'cadre's of attack dogs'. The 'confusion they purposefully generate' and the 'falsehoods they employ' in their 'misinformation effort' are 'horrific mistakes', 'intellectual tragedies', promulgated from a ''wholly corrupt' 'intellectual ghetto'. They are a 'dangerous cancer'. 'Mendacious'. 'Idiotic'. 'Creepy'. 'Silly'. 'Confused'. 'Lacking integrity'. 'Profoundly misleading'. 'Political propogandists'. 'Enemies of science.' 'Idiots'. 'Liars'. 'Bottomfeeders'.
So you see, Bilbo, flying the skull and crossbones is a Culture Pirate's way of telling his enemies that he does not recognize the conventional rules of engagement. Parlez and truce be damned.
Attack us, and your fate will be the same as Old Jolly Roger here.
Yes, SWT, your brilliant logic is irrefutable. Makalowski and Mattick cannot claim that non-coding DNA was ignored - because they themselves have been paying attention to it for OVER THREE DECADES!
These lying IDiots have been hoisted with the petards of their own scientific publications!
Are there any depths of depravity to which the IDiots will not sink?
Oops, I forgot 'Cesspool'.
Ah, the cheerleader arrives.
This is a fellow who has in the past claimed that what even he described as a 'toy' example - an 8 letter string, 'mutating' one every iteration, never mutating the sme one twice, produces a totally different 8 letter string after only 8 'generations', therefore, evolution is false.
Wouldn't worry too much about what such folk have to say about anything.
But you have no problem with argumentum ad verecundiam?
Surely they wouldn't write gay porn stories. Oh wait...
I just wanted to see if we could get this thread to shink down to a single column
I'm blending in to the margin now
Bye. I'm leaving now. Ta Ta for now
Not that that it would be a bad thing
I figure It will take 2-3 more replies before the thread disappears entirely
:) Nice work. I wondered that myself - and I agree that it was the best thing for that particular thread.
" ID advocates and other creationists claim that "Darwinists" assumed that non-coding DNA was functionless"
Don't you see the irony of your complaint, Dr. Matheson, here you are arguing against the functioning of introns, and then you complain when the DI points out a pervasive bias that you yourself exemplify!
Sure there were Darwinsits who think introns are functional and they invoke Darwinism to defend their position, but there were also Darwnists like you who argue for the functionlessness of introns and you and others also invoke Darwin to defend the "functionless" position. The fact that both camps claim Darwin explains their position only highlights the incoherence of Darwinism.
You've been repeating and defending the party line of Junk DNA arguing for the lack of function in introns. At best you are presumptuous, at worst you're dead wrong.
Is it fair to say you believe introns are mostly functionless. :-)
But this is a nearly indefensible position. Why?
If you say they are not functionless, then you have effectively retracted your claims against Meyer.
If you say they are mostly functionless, then you've demonstrated Darwinsits like you assume introns are mostly functionless and thus affirming the DI is right to assert Darwinists assume introns are functionless. This of course would be especially embarassing if we gather more evidence introns are mostly functional.
So are you prepared to insist introns are mostly functionless. :-)
PS
you should note that Casey Luskin posted a letter from Pellionisz a few years ago citing Darwinist Malcolm Simons who argues that Junk DNA is not Junk based on his belief in Darwinism. So, it would be hard to say that the DI insists every Darwinist for all time believed in Junk DNA. Thus, it would be hard to argue the DI was distorting the history of Junk DNA.
Someday maybe I'll use it as a metaphor for the accumulation of mutations in genomic regions that are invisible to selection. :-)
Ms./Mr. Cordova, your contributions here show no evidence of serious consideration of what I've written, present and past. And your servile devotion to the DI seems to lead you to pervasive incoherence and disingenuousness. (That's me being generous, btw.) It seems to me that you really shouldn't waste your time commenting here. Your public awaits you at the Cesspool. Au revoir!
Sal wrote:
"Sure there were Darwinsits who think introns are functional and they invoke Darwinism to defend their position, but there were also Darwnists like you who argue for the functionlessness of introns and you and others also invoke Darwin to defend the "functionless" position."
No, Sal, you're just lying. An integral mechanism for introns acquiring new functions is the NON-Darwinian one of drift.
"The fact that both camps claim Darwin explains their position only highlights the incoherence of Darwinism."
Where do you find Darwin explicitly mentioned in these papers from the primary scientific literature, Sal?
"You've been repeating and defending the party line of Junk DNA arguing for the lack of function in introns."
Would you please rewrite this sentence in English?
"If you say they are mostly functionless, then you've demonstrated Darwinsits like you assume introns are mostly functionless and thus affirming the DI is right to assert Darwinists assume introns are functionless. This of course would be especially embarassing if we gather more evidence introns are mostly functional."
"We," Sal? Your side lacks sufficient faith to do any work to test this alleged prediction of ID.
"you should note that Casey Luskin posted a letter from Pellionisz a few years ago citing Darwinist Malcolm Simons who argues that Junk DNA is not Junk based on his belief in Darwinism."
Wow! Somebody posted a letter in which someone else said something about what someone else said.
That's some evidence!
Davis wrote:
" An integral mechanism for introns acquiring new functions is the NON-Darwinian one "
Good one Davis, so you argue:
1. introns have function (contrary to Dr. Matheson's claim)
2. an integral part of their functioning is because of the absence of Natural Selection. ROTFL.
By the way, are you sure you're on Dr. Matheson's side?
they seem to actually believe that "Darwinists" (by this they mean people who accept evolutionary theory in just about any of its forms) still think that non-coding DNA is all junk."
Not true! It is clear from the context of their other interactions, they don't include ALL Darwinists. The citation by Sternberg of Mondal/Rasmussen is a case in point since Mondal/Rasmussen and company refers to "conserved" regions.
It should be clear they were referring to Darwinists like you who argue the existence of 100 functioning introns would be a generous estimate.
Dr. Matheson wrote: " It seems to me that you really shouldn't waste your time commenting here."
I just pointed out your errors and misrepresentations. I'd expect you'd find that valuable.
Slimy Sal wrote:
"Good one Davis, so you argue:…"
No. Try reading what I wrote for comprehension.
When did you stop beating your wife?
Congratulations Davis! You havebeen inducted into the pantheon of individuals who have been quoted out of context by Sal Cordova. It is a great honor to stand beside other notable scientists, including Charles Darwin himself! Now that you have joined this elite group, what are you going to do?
Davis wrote:
" An integral mechanism for introns acquiring new functions is the NON-Darwinian one "
The reference to Darwinists defending intron function was in regards to in the conservation of function as in CONSERVED regions, not in acquisition.
The Mondal/Rasmussen paper I cited is an example. The mechanism of acquisition of function is mostly irrelevant to how Mondal/Rasmussen made their inference. You're the one with comprehensional issues.
But in any case you only hurt the position you were trying to defend in addition to illustrating for the readers your lack of comprehension of the argument I actually put forward, namely, certain Darwinists have argued for intron functionality because of "conserved" regions.
Laugh at his dishonesty, mainly.
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