Junk DNA is still junk

Interesting, a good summary.

Opponents of evolutionary biology are always saying that “Intelligent Design predicts that there is no junk DNA”. They also say that ID is not religion but a straightforward scientific theory. Now I can think of theological arguments against the existence of junk DNA (along the lines of “No self-respecting Deity would ...”).

But if we rule out that theological argument, exactly where in ID do this supposed “prediction” come from? I don't recall anything in the writings of Dembski or Behe that makes any such prediction. Does anyone have a non-theology source for it?

Joe Felsenstein said: Interesting, a good summary. Opponents of evolutionary biology are always saying that “Intelligent Design predicts that there is no junk DNA”. They also say that ID is not religion but a straightforward scientific theory. Now I can think of theological arguments against the existence of junk DNA (along the lines of “No self-respecting Deity would ...”). But if we rule out that theological argument, exactly where in ID do this supposed “prediction” come from? I don't recall anything in the writings of Dembski or Behe that makes any such prediction. Does anyone have a non-theology source for it?

Does anyone have a non-theology source for it?

How can ID predict that there is no junk DNA? Such a prediction can only be made with the assumption of a design that minimizes genomic waste. But that assumption is based on speculation on the nature of the designer. And that's a non-no, or so the IDers keep telling us.

Genomic waste? What fraction of a cell's mass is its DNA? If the mass of the DNA is tiny compared to the whole cell, and doesn't require excessive amount of resources to produce and maintain it, then where's the waste?

Henry J said: Genomic waste? What fraction of a cell's mass is its DNA? If the mass of the DNA is tiny compared to the whole cell, and doesn't require excessive amount of resources to produce and maintain it, then where's the waste?

What I'm wondering is how the cost of having the unused DNA compares to the total cost of running the cell. That seems to me to be more important than comparing the cost of the junk DNA to the cost of the functional DNA.

JohnK said:

Does anyone have a non-theology source for it?

Since ID'ers are quick to say there is no reason to expect optimal designs, I believe the motivation for the prediction is "functionality would show scientists have been wrong, so ID must be right." Pretty much the stock ID negative argument, posing for the rubes as a positive hypothesis. As far back as around 2000, Johnny Wells and S. Meyer were predicting DNA will almost all be functional. Here's poodle Casey Luskin summarizing ID predictions. Note the last prediction and footnote 6 -- apparently this falsifies ID once and for all. Cough.

Aha! ID has always predicted that there would be loads of junk DNA, because the human genome has been degrading ever since the Fall, uh, I mean, since the designer designed us! And we've always been at war with Eastasia!

Aagcobb said: Aha! ID has always predicted that there would be loads of junk DNA, because the human genome has been degrading ever since the Fall, uh, I mean, since the designer designed us! And we've always been at war with Eastasia!

It doesn’t get any better than this!

weren't you banned from here eons ago, John?

do you truly love it so?

aren't you having enough fun arguing with yourself on any of your own blogs?

johnadavison said: Neo-Darwinism is as dead as the proverbial doornail. It has become perfectly obvious that phylogeny was planned from beginning to end and the end is any time now.

What I’m wondering is how the cost of having the unused DNA compares to the total cost of running the cell. That seems to me to be more important than comparing the cost of the junk DNA to the cost of the functional DNA.

I once saw a comment someplace that large genomes tend to be correlated with large cells, and that cell size may have selective advantages.

So junk DNA may actually have a function, just as wadded-up pages of newspapers used for packing something fragile in a box have a function. In either case, it's not there to be read.

The genome would be a book that was 75%+ full of gibberish or short repetitive sequence.

heh, I often think most books are.

the end is any time now.

wait, how old are you again, John?

JohnK said: Since ID'ers are quick to say there is no reason to expect optimal designs,

MrG said: I once saw a comment someplace that large genomes tend to be correlated with large cells, and that cell size may have selective advantages.

And before that, Masterson, J. 1994. Stomatal Size in Fossil Plants: Evidence for Polyploidy in Majority of Angiosperms. Science 264:421-424.

Abstract: Three published estimates of the frequency of polyploidy in angiosperms (30 to 35 percent, 47 percent, and 70 to 80 percent) were tested by estimating the genome size of extinct woody angiosperms with the use of fossil guard cell size as a proxy for cellular DNA content. The inferred chromosome numbers of these extinct species suggest that seven to nine is the primitive haploid chromosome number of angiosperms and that most angiosperms (approximately 70 percent) have polyploidy in their history.

Ichthyic said: the end is any time now. wait, how old are you again, John?

I wonder if the nonfunctional DNA increases the amount of space per useful gene, which might reduce the amount of delays due to DNA readers getting in each others way?

Henry

The bottom line, though, is the genome is mostly dead, transcriptionally. The junk is still junk.

johnadavison said: I thank Wes or Pee Zee or whoever is responsible for allowing me once again to opine here. I am disappointed that Ichthyic had to stoop to refer to my age. Since he asked, I will be 82 on June 25 next. Let me quote one of my contemporaries. "You ain't heard nothin' yet." Al Jolson I have a book coming out soon which is a collection of my unpublished papers and essays dealing with the great mystery of phylogeny. I expect it to be reviewed here. In the meantime I recommend the following link - http://jadavison.wordpress.com/2008/01/06/predictions/#comments For a sample of what to expect, especially #249 and several preceding messages.

kakapo said:

MrG said: I once saw a comment someplace that large genomes tend to be correlated with large cells, and that cell size may have selective advantages.

e.g. “Origin of avian genome size and structure in non-avian dinosaurs,” Organ et al., Nature v 446 p 180 (8 March 2007)

Intelligent Designer said: This statement assumes that DNA is only functional if it is transcribed.

This statement assumes that DNA is only functional if it is transcribed.

Junk DNA is “wasteful”, though, if you think of the genome like you would think of a book, like ID advocates do. The genome would be a book that was 75%+ full of gibberish or short repetitive sequence.

johnadavison said: I see I was not allowed to respond to Dale Husband's vicious attack on my integrity and sanity. My lengthy response was deleted after its brief appearance. That has become a trademark of Panda's Thumb policy of intolerant protectionism and intellectual bigotry. Let's see if this will be allowed to stand.

Dave Wisker said:

This statement assumes that DNA is only functional if it is transcribed.

Eliminating transcription greatly narrows down the functional possibilities.

This statement assumes that DNA is only functional if it is transcribed.

And how else would DNA have a function?

I don't know why anti-evolutionists worry about whether junk DNA is useful or not in the first place; neither presence nor absence of junk DNA is logically implied by the hypothesis that life was in some way engineered.

Answering that sort of question requires a lot of detail on the methods, motives, and limitations of the engineer(s) that did it, so a wrong answer on this question would mean only that they had the details wrong; it wouldn't impact their central concept.

Natman said: Onto subject matter: I'm always wary about anything science-y saying that something isn't needed, or is 'junk'. It's better to hedge such statements with a proviso that it's junk according to current theories. Otherwise, by making such absolutes, there is the risk that at somepoint in the future, a function may be found (even it's only for cell packing), and the cDesignists will have something to wave around and assume it proves something. One of the big divisions between informed scientific opinion and dogmatic creationist rantings is the ability of science to never hold to absolutes, to always be willing to change and adapt if a better and more plausible idea is put forwards.

Some might be interested to know that Wikipedia no longer has a entry for Junk DNA. That link now transfers automatically to an entry on Non-coding DNA. Calling it junk in the first place was a blunder.

Intelligent Designer said: Some might be interested to know that Wikipedia no longer has a entry for Junk DNA. That link now transfers automatically to an entry on Non-coding DNA. Calling it junk in the first place was a blunder.

Intelligent Designer said: Some might be interested to know that Wikipedia no longer has a entry for Junk DNA. That link now transfers automatically to an entry on Non-coding DNA. Calling it junk in the first place was a blunder.

harold said: In fact, mice lacking large regions of junk DNA are a major model in ongoing research. Such mice are perfectly viable at birth, ruling out the idea that the deleted DNA performs a function necessary for life.

Natman said: Next they'll be saying that creationist stories aren't based on any provable evidence and are merely the result of a mortal sentient creature trying to make sense of the world around them.

Intelligent Designer said: The fact that you candelete some mouse DNA and still have a viable mouse doesn't mean it is junk. Researchers have created mice that aren't afraid of cats (so they are dumber mice). I don't know if this was done by deletion though. Maybe someone else knows.

Another possible function of non-coding DNA could be for adaptive capacitance.

Wikipedia is grossly wrong. Non-coding DNA and junk DNA are [b]not[/b] synonymous terms, and never have been. Regulatory sequences, for instance, are non-coding, but have never been characterized as junk DNA.

The Wikipedia article says that much of the non-coding DNA is junk; it doesn't say all of it. It has a section discussing the origin and usage of the term "junk DNA".

PZ Myers said: Wikipedia is grossly wrong. Non-coding DNA and junk DNA are [b]not[/b] synonymous terms, and never have been. Regulatory sequences, for instance, are non-coding, but have never been characterized as junk DNA.

The fact that you candelete some mouse DNA and still have a viable mouse doesn’t mean it is junk.

But the data support neither the ludicrous and dishonest claims of creationists (of course), nor the oversimplification “since a creationist said it should have a function and since we colloquially call it ‘junk’, therefore it must have no function or activity whatsoever”. In fact, mice lacking large regions of junk DNA are a major model in ongoing research. Such mice are perfectly viable at birth, ruling out the idea that the deleted DNA performs a function necessary for life. But they also differ from other mice in important, if subtle, ways.

I would argue that your hypothesis has been tested and found to be wrong. Lenski has been tracking DNA changes in his e coli specimens for 50,000 generations now. If the citrate-eating mutation weren’t actually a mutation, but rather the turning on of some previously non-coding part of the existing genome, he’d have reported it.

The theory of evolution is not with some sort of functionality for some or all of non-coding DNA.

Intelligent Designer said:

PZ Myers said: Wikipedia is grossly wrong. Non-coding DNA and junk DNA are [b]not[/b] synonymous terms, and never have been. Regulatory sequences, for instance, are non-coding, but have never been characterized as junk DNA.

No. Wikipedia is absolutely right. Junk DNA is outdated and unfortunate terminology and should be dropped from our vocabulary.

PZ Myers said: Wikipedia is grossly wrong.

Is it that big an error for "junk DNA" to be relegated to a chapter in the article on "non-coding DNA"?

Natman -

Actually, I don't at all agree that Wikipedia is wrong here, and I find it to be a very good source for terse, articulate, generally accurate summaries of scientific topics (among other things). A good article will have appropriate references to the original literature, which will themselves have reference sections, so anyone can go deeper with ease.

PZ misunderstood, and thought that Wikipedia had confounded non-coding regulatory elements with the different type of non-coding DNA sometimes referred to as "junk" DNA, which would indeed have been a gross error. That has been cleared up. Wikipedia did not contain this error.

Dale Husband -

Whether or not something is called "junk" is a subjective decision. I could call the genes for the most basic and critical metabolic functions "junk" if I felt like it.

There are eukaryotic genes which have arisen from non-coding sequences and mice without certain non-coding sequences are viable but not exactly the same as the mice with the sequences. Whether any of this counts as "function" or not, perhaps another subjective decision, I don't know.

However, if we dogmatically, and against the evidence, suggest that all non-coding DNA is 100% irrelevant, not to say you're doing that but if we do, we risk giving creationists a freebie, allowing them to be "right for the wrong reason".

ritebrother said: One postulate (the current status of which I don't know) is that "excess" non-transcribed DNA provides a buffer against ionizing radiation by keeping the resulting coding region mutation frequency low.

Ian Musgrave said: a) We know what the DNA is; in humans around 2% codes for proteins, another 2-3% either codes for things like t-RNA, ribosomal RNA, small nucleolar RNA or represents binding sites for regulatory factors. About 4% is broken viruses; roughly another 4% are broken genes (like the non-functional ascorbic acid sythetase gene). The remainder represents highly repetitive DNA like LINES and SINES or ALU sequences.

Intelligent Designer -

First of all, you need a different name, unless you really are a creo, because the one you have now is guaranteed to rub people the wrong way.

I find both of your thoughts interesting. I also think they are both likely to be wrong.

A given absolute quantity of ionizing radiation would provide the energy to theoretically drive up to a given number of mutations. For that reason alone the presence of less relevant base pairs could stochastically shield gene sequences. Your assessment would be correct only if the energy amount of ionizing radiation exposure were always in excess of that required to mutate every base pair in the genome.

As an analogy, imagine if I have a deck of playing cards, and a monster is going to rip up some of the cards. I want a mechanism to make sure he rips up as few real cards as possible. If I add hundreds of blank cards to the deck, and he is equally likely to rip them up, it (imperfectly) protects the real cards. The only way it doesn't is if the monster always can and always will rip up all the cards, no matter how many blanks I add.

I am not endorsing the "protection" hypothesis, I am trying to explain it.

Furthermore, the genome is not physically structured as a one dimensional string of nucleotides. "Junk" DNA could be positioned in a way to be more exposed.

Also, the virus genomes in non-coding DNA are generally so degraded that they no longer code for viable viruses. In fact, if that weren't the case, the viruses they code for would be expressed in our bodies. Viral-induced pathology nearly always requires intact, viable virus reproduction. It is massively, overwhelmingly more likely that these are exactly what they look like - "fossil" remnants of viral infections that our distant past ancestors once had.

The bottom line, though, is the genome is mostly dead, transcriptionally. The junk is still junk.

harold said: Intelligent Designer - First of all, you need a different name, unless you really are a creo, because the one you have now is guaranteed to rub people the wrong way.

sciencedaily.com: Remarkably, the new research, recently published in Current Biology, shows that these early estimates were spot on - in total, we all carry 100-200 new mutations in our DNA. This is equivalent to one mutation in each 15 to 30 million nucleotides. Fortunately, most of these are harmless and have no apparent effect on our health or appearance.

JH: The problem that I have with junk DNA is that it must be energetically expensive to keep it hanging round if it does no good, and if bacteria have a method of weeding it out why don't we bother?

Nature. 2004 Oct 21;431(7011):988-93. Megabase deletions of gene deserts result in viable mice. Nóbrega MA, Zhu Y, Plajzer-Frick I, Afzal V, Rubin EM. DOE Joint Genome Institute Walnut Creek, California 94598, USA. Abstract The functional importance of the roughly 98% of mammalian genomes not corresponding to protein coding sequences remains largely undetermined. Here we show that some large-scale deletions of the non-coding DNA referred to as gene deserts can be well tolerated by an organism. We deleted two large non-coding intervals, 1,511 kilobases and 845 kilobases in length, from the mouse genome. Viable mice homozygous for the deletions were generated and were indistinguishable from wild-type littermates with regard to morphology, reproductive fitness, growth, longevity and a variety of parameters assaying general homeostasis. Further detailed analysis of the expression of multiple genes bracketing the deletions revealed only minor expression differences in homozygous deletion and wild-type mice. Together, the two deleted segments harbour 1,243 non-coding sequences conserved between humans and rodents (more than 100 base pairs, 70% identity). Some of the deleted sequences might encode for functions unidentified in our screen; nonetheless, these studies further support the existence of potentially 'disposable DNA' in the genomes of mammals.

"...we haven't found a function for any of them yet..."

Those few words pack a very big punch -even if you arent an optimist, wishful thinker, open-minded skeptic....

Lion (IRC)

Curiously, PZ has bothered to mention Richard Sternberg's response to Ayala and Falk on this subject.

PZ, you're not by any chance peeved that you were not invited to the discussions amonth warring theists?

On second thought, a dangerous notion.

But just in case, PZ. Would you mind giving your take on how and where Sternberg is wrong on the apparent functionality of 'junk' DNA?

In case you may have 'lost' the links, here are the three posts Richard wrote on the subject in March of this year:

http://www.evolutionnews.org/2010/03/ayala_and_falk_miss_the_signs.html

http://www.evolutionnews.org/2010/03/signs_in_the_genome_part_2.html

http://www.evolutionnews.org/2010/03/beginning_to_decipher_the_sine.html

Looking forward to that crushing post where you score yet another triumph, embarrassing the theists for the nth time.

Sorry, that should read 'PZ has hasn't bothered....'

There seems to be some confusion about the definitions of "junk DNA" and "non-coding DNA", and it's persisted even after PZ's response. Please, people.

Junk DNA is DNA in which particular sequences have no function (though I would allow bulk functions, like the possible selection for cell size mentioned above). We can distinguish junk DNA not because it has no known function but because it evolves at the mutation rate, i.e. neutrally.

Non-coding DNA is just that: DNA that isn't translated into protein using the genetic code. A fair amount of non-coding DNA has a function: functional RNAs, regulatory sequences, and a few other conserved regions whose functions are unknown (but we know they have functions because they evolve more slowly than the mutation rate).

All junk DNA is non-coding, but not all non-coding DNA is junk, and it would be foolish to dispose of either term, since they have useful and separate meanings.

The paper looks at poly-A+ RNA, so this isn't really the book on transcription.

I recall learning recently about how DNA transcription really works. In all the idealized renderings I'd seen previously, the DNA is unzipped into long straight rails that the RNA enzymes work on. But (IIRC) the DNA double helix is normally wound and folded rather tightly (and precisely), as though on a spool, and the double helix is only "loosened" enough for the transcription process. More importantly, it's typically not the actual sequence itself (of either DNA, RNA, or the resulting protein) that is important, but rather it is the 3 dimensional and electrical structure of the molecules that make them useful. Also, with the multiple windings of DNA, the interesting interactions can sometimes be between pieces of DNA that are not right "next to" each other in terms of base-pair separation, but which might end up "next to" each other physically when wound and folded in their normal manner. I wonder (as harold suggested earlier) whether the "junk" DNA might serve some sort of "structural" or "buffer" function, keeping other "functional" pieces at just the right separation for proper transcription or methylation . The actual content of (or kinds of base pairs in) the "buffer" might be immaterial, and so does not need to be conserved. Perhaps what might be important is the number of base pairs in the "buffer" region? Has there been any research along those lines?

Of course, I could be remembering this incorrectly, and ending up way off base here. I'm no biologist. Just a curious amateur.

On a slightly different topic, while there is a lot of DNA that doesn't code for anything in a mature cell, have we learned enough about evo-devo yet to say whether some of this "junk" DNA doesn't have some function in the early development cycles of the embryo? (Though, finding that much of the "junk" DNA is not conserved, probably argues against that idea anyway.)

Junk DNA is DNA in which particular sequences have no function (though I would allow bulk functions, like the possible selection for cell size mentioned above). We can distinguish junk DNA not because it has no known function but because it evolves at the mutation rate, i.e. neutrally.

Testing noncoding DNA for function is experimentally within reach. It’s been done. Someone deleted megabases of DNA from the mouse genome and then made cloned mice. No phenotype, nothing happened except the DNA is gone.

harold said: The evidence that the sequence of junk DNA doesn't matter is very strong, as you note. However, non-coding regions have acquired regulatory elements and given rise to genes.

harold wrote:

"ID/creationists are forced by their ideology to deny the evidence and insist on “function” for all of non-coding DNA.

The rest of us can go with the evidence, but the evidence doesn’t necessarily suggest that junk DNA has no impact whatsoever."

Right. But the thing is that the rest of us are not forced to assume that all the DNA was poorly designed either. The fact that DNA can evolve cannot be used as evidence that it cannot evolve.

Raven said - Testing noncoding DNA for function is experimentally within reach. It’s been done. Someone deleted megabases of DNA from the mouse genome and then made cloned mice. No phenotype, nothing happened except the DNA is gone. Harold: No morphologic phenotype changes, but fascinatingly, there may or may not be some subtle but important metabolic changes when some non-coding regions are deleted from mice.

John Harshman -

"However" because once a segment of DNA gets the regulatory elements to be a gene, and can at least potentially be a template for expression of RNA and/or protein (depending on regulation), then that sequence might (or might not) become subject to selective pressure related to whatever impact the RNA or protein might have on the cell.

In contrast to a completely non-regulatory, non-coding sequence, which would probably be under very little to no selective pressure directly related to the nucleotide sequence.

(It's also true that junk DNA overall does not have entirely random sequence. It's full of repetitive elements. For whatever reason, those repetitive elements were "selected" to be spread around the genome, relative to other sequences. I have no idea why this is - it could be that these particular sequences are simply more likely to provoke duplication mutations when they are being replicated.)

Obviously, we are in complete agreement on this subject. So-called junk DNA does not code for genes, by definition. The sequence of junk DNA in general is not subject to the selective pressure the way the sequences of many genes are, which is strong evidence that the exact nucleotide sequence of junk DNA is not germane to any major cellular function.

However, some or all of this DNA may have impact on the cells that contain it. It is a poorly understood area. The mouse evidence both demonstrates that the (studied) areas of junk DNA do not contain any elements which are critical to basically normal mouse development and physiology. Yet it also illustrates a possible subtle but relevant metabolic impact of having or lacking the sequences that were studied. The fact that genes can arise from such DNA is another potential type of impact.

The arguments of ID/creationists on this subject reflect deep ignorance, commitment to a rigid, irrational ideology, and the lack of ethical character which permits them to deliberately "fake" scientific authority while actually hurling out verbose nonsense.

Indeed, the very existence of junk DNA reveals their hypocrisy. They claim that they merely seek evidence for some non-specific "designer". Yet they implicitly seek to imbue this "designer" with the traits of their post-modern, politically motivated god. The only reason junk DNA is a challenge to them is because a "benign", human-like designer (even by their twisted idea of what is "benign") would not be expected to create it.

Raven -

Yes, we are in total agreement, and it is clear that much of the repetitive sequence type of junk DNA, for example, can vary greatly between individuals with literally no apparent impact whatsoever.

It is an interesting topic, among many, for rational people, and one of many insurmountable problems for creationists.

Scott said: "...it’s typically not the actual sequence itself (of either DNA, RNA, or the resulting protein) that is important, but rather it is the 3 dimensional and electrical structure of the molecules that make them useful."

Can someone tell me if that's correct? I was under the impression that the sequence of DNA and consequently messenger RNA was extremely important, and that the "3 dimensional and electrical structure of the molecules" was most salient with proteins.

hoary puccoon -

It is absolutely the sequence of nucleotides in a gene that codes, through the intermediate of mRNA, for the amino acid sequence of the protein. Downstream processing may impact on whether and where the protein is truncated, glycosylated, etc. The amino acid sequence of the protein, in conjunction with chemical modifications like glycosylation, if present, will determine its three dimensional structure. Proteins "fold" spontaneously into their three dimensional structure.

Regulatory elements work largely through nucleotide sequence as well.

Chemical modifications of individual nucleotides, such as methylation, can be important as well.

“3 dimensional and electrical structure of the molecules” has a lot to do with how eukaryotic chromosomes are packaged into the nucleus, though. http://en.wikipedia.org/wiki/Chromosome

harold--

Thanks. You confirmed what I had understood.

hoary,

Scott is referring to the fact that genomes are packaged three dimensionally in space, and in certain instances a specific conformation is important for a process. For example, bringing a very distant regulatory region (of specific sequence) close to another region (of specific sequence). Here both the sequence of the DNA and the arrangement of the chromosomal ultrastructure are important.

Pinko Punko--

Thanks to you also. Knowing more about the history of science than about science, it's amazing to me what is now known.

Henry J said: I don't know why anti-evolutionists worry about whether junk DNA is useful or not in the first place; neither presence nor absence of junk DNA is logically implied by the hypothesis that life was in some way engineered. Answering that sort of question requires a lot of detail on the methods, motives, and limitations of the engineer(s) that did it, so a wrong answer on this question would mean only that they had the details wrong; it wouldn't impact their central concept.

According to the paper, only about 50% of the functional non-coding elements are constrained across all mammals. It would be very easy for the Creationists to say, “Look! If this is so important why didn’t natural selection preserve it!”

Pinko Punko said: hoary, Scott is referring to the fact that genomes are packaged three dimensionally in space, and in certain instances a specific conformation is important for a process. For example, bringing a very distant regulatory region (of specific sequence) close to another region (of specific sequence). Here both the sequence of the DNA and the arrangement of the chromosomal ultrastructure are important.

Let's call a spade a spade. A good old boys club is just that. Peer review shmeer review. If I can get an alliance of like minded people to write articles agreeing with my premise that junk DNA lead to vertical and not horizontal stripes on zebras, then, according to the good old boys club rules, I must be right! You can call certain strands of DNA junk, but these strands exist, and I'll assert that the label has an agenda behind it. If DNA, that is not "junk" is the "worthy" DNA, then let's apply this to all the scientists perpetuating peer reviewed articles, these would be the "worthy scientists". Are the remainder of scientists merely, "junk scientists"? I browsed your Expelled category and the length to which you defend your theory of evolution is no surprise. It is, after all your religion. What I could not ignore is the reality, and I need no peer review for this observation, that the ID scientific community embarrassed the "...life came to earth on the back's of crystals..." evolutionary scientific world view community.

GODISNOWHERE said: Let's call a spade a spade. A good old boys club is just that. Peer review shmeer review. If I can get an alliance of like minded people to write articles agreeing with my premise that junk DNA lead to vertical and not horizontal stripes on zebras, then, according to the good old boys club rules, I must be right! You can call certain strands of DNA junk, but these strands exist, and I'll assert that the label has an agenda behind it. If DNA, that is not "junk" is the "worthy" DNA, then let's apply this to all the scientists perpetuating peer reviewed articles, these would be the "worthy scientists". Are the remainder of scientists merely, "junk scientists"? I browsed your Expelled category and the length to which you defend your theory of evolution is no surprise. It is, after all your religion. What I could not ignore is the reality, and I need no peer review for this observation, that the ID scientific community embarrassed the "...life came to earth on the back's of crystals..." evolutionary scientific world view community.

GODISNOWHERE said: If I can get an alliance of like minded people to write articles agreeing with my premise that junk DNA lead to vertical and not horizontal stripes on zebras, then, according to the good old boys club rules, I must be right!

I browsed your Expelled category and the length to which you defend your theory of evolution is no surprise. It is, after all your religion.

What I could not ignore is the reality, and I need no peer review for this observation, that the ID scientific community embarrassed the "...life came to earth on the back's of crystals..." evolutionary scientific world view community.

MrG said:

I browsed your Expelled category and the length to which you defend your theory of evolution is no surprise. It is, after all your religion.

Bob no. My religion is standup comedy.

MrG said:

What I could not ignore is the reality, and I need no peer review for this observation, that the ID scientific community embarrassed the "...life came to earth on the back's of crystals..." evolutionary scientific world view community.

I can't disagree, due to the fact that after repeated readings I have absolutely no idea what that means.

Stanton said: She’s actually dead, but, people either can’t tell, or they just don’t have the heart to tell her.

Stanton said: I think the moronic troll is trying to say ...

GODISNOWHERE said: Let's call a spade a spade. A good old boys club is just that. Peer review shmeer review. If I can get an alliance of like minded people to write articles agreeing with my premise that junk DNA lead to vertical and not horizontal stripes on zebras, then, according to the good old boys club rules, I must be right!

You can call certain strands of DNA junk, but these strands exist, and I'll assert that the label has an agenda behind it.

If DNA, that is not "junk" is the "worthy" DNA, then let's apply this to all the scientists perpetuating peer reviewed articles, these would be the "worthy scientists". Are the remainder of scientists merely, "junk scientists"?

I browsed your Expelled category and the length to which you defend your theory of evolution is no surprise. It is, after all your religion.

What I could not ignore is the reality, and I need no peer review for this observation, that the ID scientific community embarrassed the "...life came to earth on the back's of crystals..." evolutionary scientific world view community.

Ian Musgrave said: There are several lines of evidence that most of the DNA in humans and other organisms is junk. a) We know what the DNA is; in humans around 2% codes for proteins, another 2-3% either codes for things like t-RNA, ribosomal RNA, small nucleolar RNA or represents binding sites for regulatory factors. About 4% is broken viruses; roughly another 4% are broken genes (like the non-functional ascorbic acid sythetase gene). The remainder represents highly repetitive DNA like LINES and SINES or ALU sequences.

(shrug) Okay. All you have to do is show what all these repetitive or non-coding or apparently non-functional regions actually do, and why they're not really just broken genes, dead retroviri, and so on, even though that's what they appear to be to anyone who knows what they're talking about.

Until then, I'm going to side with the men and women who make it their livelihood to work with and understand this stuff, rather than armchair quarterbacks and Aristotlean mind-wankers.

(See, I knew we'd get to the "DNA is like computer code" sooner or later. To a man with an ax, everything looks like a tree.)

Well, repetition isn't unique to software binaries. It is found in all kinds of information. Open your computer and look at the circut boards. What you will find are the same jobbers being used over and over again. Same thing with the English language or any written language. Repetition is a hallmark of information, not the other way around.

fnxtr said: I knew we'd get to the "DNA is like computer code" sooner or later.

Intelligent Designer--

We all get why a cdesign proponentsist like yourself would be so enamored of repetition-- it's all the scientific creationist crowd does.

But could you put aside for one moment how much the Christian dominionists are paying you, and look at this from the point of view of the poor scientist in the lab? How does the fact that there are useful repetitive elements in a computer program translate into publishable scientific research in biology? Scientists are arguing for Junk DNA because they can't find any way in which that DNA is coded into anything useful. If they do find it's useful in some way, they will be eager to publish those results, and the peer-reviewed journals will be eager to accept them.

Blathering about an analogy to computer code adds nothing to the research one way or the other. I could argue that evolution is true because the electrical system in my 20-year-old sailboat looks like it evolved, instead of being designed (worse luck!) But that would be no help to, say, a paleontologist trying to tease out the relationships between hominid fossils.

What you wrote did nothing except make ID look like a vacuous word game. If that was your intent, of course, please proceed.

Paul Zachary, please give us your understanding of the term "junk DNA" so that it does not become some superfluous idea without meaning. Can you please provide a test or experiment to verify whether a sequence is in actual fact "junk DNA".

I am looking forward to your answer so that I can commence in the lab to actually try and find this so-called "junk DNA".

Curious said: Can you please provide a test or experiment to verify whether a sequence is in actual fact "junk DNA".

Check and mate. Well played, eric.

Intelligent Designer said: Brought over from another blog entry:

Ian Musgrave said: There are several lines of evidence that most of the DNA in humans and other organisms is junk. a) We know what the DNA is; in humans around 2% codes for proteins, another 2-3% either codes for things like t-RNA, ribosomal RNA, small nucleolar RNA or represents binding sites for regulatory factors. About 4% is broken viruses; roughly another 4% are broken genes (like the non-functional ascorbic acid sythetase gene). The remainder represents highly repetitive DNA like LINES and SINES or ALU sequences.

I don't think we should rush to conclude that highly repetitive DNA is junk.

I know it would be a mistake to think that about software. If you look at software executables (like .exe and .dll files on Windows computers) they are full of repeated sequences. You may have written a program yourself. If so, you would certainly be familiar with the concept of a subroutine or a method. At the assembly level, whenever a subroutine is called registers are pushed on the stack, when one returns they are popped of the stack. The code to push and pop registers is automatically generated by the complier and is therefore not apparent at the source code level. This translates into a massive amount of simplistic repetition at the binary level. These kinds of repetitive sequences would probably be classified as SINES by geneticists trying to understand the binary code.

While this kind of code doesn’t map to any kind of a program function it is essential.

You may also know that most software developers these days work with object oriented languages where inheritance and polymorphism are used to develop hierarchies of classes. At the source code level inheritance enables developers to reuse source code without retyping it. However, when source code is compiled into binary form the result is a massive amount of repetition, but of a more sophisticated nature than that of just pushing and popping registers. These kinds of repetitive sequences would probably be classified as LINES.

hoary puccoon said: Intelligent Designer-- But could you put aside for one moment how much the Christian dominionists are paying you, and look at this from the point of view of the poor scientist in the lab? How does the fact that there are useful repetitive elements in a computer program translate into publishable scientific research in biology?

Randy, I would draw your attention to Pharyngula, where Myers has just written an entire post demolishing your claims. He writes well, though I disagree with his theological position; you will find that he and commenters have exhaustively dealt with your errors and misconceptions.

Malchus said: Randy, I would draw your attention to Pharyngula, where Myers has just written an entire post demolishing your claims. He writes well, though I disagree with his theological position; you will find that he and commenters have exhaustively dealt with your errors and misconceptions.

Curious said: Paul Zachary, please give us your understanding of the term "junk DNA" so that it does not become some superfluous idea without meaning. Can you please provide a test or experiment to verify whether a sequence is in actual fact "junk DNA". I am looking forward to your answer so that I can commence in the lab to actually try and find this so-called "junk DNA".

Intelligent Designer said:

Malchus said: Randy, I would draw your attention to Pharyngula, where Myers has just written an entire post demolishing your claims. He writes well, though I disagree with his theological position; you will find that he and commenters have exhaustively dealt with your errors and misconceptions.

And just like last time, PZ is making his argument by putting words in my mouth. Also PZ did not site any facts in his post that I am not aware of.

Malchus said: I continue to pray for your redemption, but I fear hell awaits you on your present course.

Is anyone aware of the fact that Dr. William Dembski, in his book "The Design Revolution", makes it quite clear that ID is completely consistent with the expectation that junk DNA will clutter the genome?

Read the following (emphasis added). After explaining how intelligent designers (human computer programmers) were apt to leave dead code in their programs, Dr. Dembski explains:

However, the dead code can happily sit in the source code (as perhaps can the 'junk' DNA stay in the DNA) forever - doing nothing but causing confusion to later intelligent observers - engineers who must update the program for example.

http://www.iscid.org/encyclopedia/Optimal_Design,_Argument_From

aiguy said: Is anyone aware of the fact that Dr. William Dembski, in his book "The Design Revolution", makes it quite clear that ID is completely consistent with the expectation that junk DNA will clutter the genome?

aiguy said: Is anyone aware of the fact that Dr. William Dembski, in his book "The Design Revolution", makes it quite clear that ID is completely consistent with the expectation that junk DNA will clutter the genome? Read the following (emphasis added). After explaining how intelligent designers (human computer programmers) were apt to leave dead code in their programs, Dr. Dembski explains: However, the dead code can happily sit in the source code (as perhaps can the 'junk' DNA stay in the DNA) forever - doing nothing but causing confusion to later intelligent observers - engineers who must update the program for example. http://www.iscid.org/encyclopedia/Optimal_Design,_Argument_From

DS (and Malchus), you misunderstood completely.

The point is that while IDers claim that ID predicts that junk DNA will be found to be functional, it turns out that their leading light Dr. Dembski himself had already admitted that Junk DNA (or its absence) is perfectly consistent with ID! His book "The Design Revolution" was published in 2004, before IDers started blabbing about these junk DNA "predictions". I guess they just didn't notice that Dembski had already claimed that junk DNA was no problem for ID. So for IDers to now suggest that their theory "predicted" that junk DNA was actually functional is even dumber, considering that Dembski had already discounted any such prediction.

Get it?

aiguy said: DS (and Malchus), you misunderstood completely. The point is that while IDers claim that ID predicts that junk DNA will be found to be functional, it turns out that their leading light Dr. Dembski himself had already admitted that Junk DNA (or its absence) is perfectly consistent with ID! His book "The Design Revolution" was published in 2004, before IDers started blabbing about these junk DNA "predictions". I guess they just didn't notice that Dembski had already claimed that junk DNA was no problem for ID. So for IDers to now suggest that their theory "predicted" that junk DNA was actually functional is even dumber, considering that Dembski had already discounted any such prediction. Get it?

aiguy said: DS (and Malchus), you misunderstood completely. The point is that while IDers claim that ID predicts that junk DNA will be found to be functional, it turns out that their leading light Dr. Dembski himself had already admitted that Junk DNA (or its absence) is perfectly consistent with ID! His book "The Design Revolution" was published in 2004, before IDers started blabbing about these junk DNA "predictions". I guess they just didn't notice that Dembski had already claimed that junk DNA was no problem for ID. So for IDers to now suggest that their theory "predicted" that junk DNA was actually functional is even dumber, considering that Dembski had already discounted any such prediction. Get it?

Malchus said: Since the analogy between DNA and computer code is invalid ...

aiguy said: DS (and Malchus), you misunderstood completely. The point is that while IDers claim that ID predicts that junk DNA will be found to be functional, it turns out that their leading light Dr. Dembski himself had already admitted that Junk DNA (or its absence) is perfectly consistent with ID! His book "The Design Revolution" was published in 2004, before IDers started blabbing about these junk DNA "predictions". I guess they just didn't notice that Dembski had already claimed that junk DNA was no problem for ID. So for IDers to now suggest that their theory "predicted" that junk DNA was actually functional is even dumber, considering that Dembski had already discounted any such prediction. Get it?

Intelligent Designer said: [snip bit about non-coding DNA ..."About 4% is broken viruses; "...] We know that virus can target and kill some cells while leaving other cells alone. If a cell malfunctions in a certain way it could send out a chemical signal that would trigger the activation of a dormant virus designed to kill that type of defective cell.

Stimpy sez:

PZ did not site [sic] any facts in his post that I am not aware of.

more's the pity then, since we said the same things to you years ago, and you're still making the same basic errors in fact and logic.

I feel sorry for you, I truly do, that since apparently this is such an important issue to you, you would fail to even bother to try and learn the basic biology that would inform you enough to make cogent statements.

that you see no problem with stumbling blindly forward in your attempts to outdo Don Quixote suggests to me you have mental issues to deal with.

deal with that first, then take some classes in basic biology and genetics, THEN come back if you manage to produce a model, or an argument, that makes sense.

Ichthyic said: Stimpy sez: PZ did not site [sic] any facts in his post that I am not aware of. more's the pity then, since we said the same things to you years ago, and you're still making the same basic errors in fact and logic. I feel sorry for you, I truly do, that since apparently this is such an important issue to you, you would fail to even bother to try and learn the basic biology that would inform you enough to make cogent statements. that you see no problem with stumbling blindly forward in your attempts to outdo Don Quixote suggests to me you have mental issues to deal with. deal with that first, then take some classes in basic biology and genetics, THEN come back if you manage to produce a model, or an argument, that makes sense.

ID in the sense that the Intelligent Design movement makes use of is intellectually vacuous - without specifying characteristics of the designer, any and all observations are compatible with intelligent design.

There is an already large and growing set of parallels of structure and function between genome/proteome and human language- much more than any of you have been led to believe.

Sequences outside of protein-coding sequences (and some inside) act like grammar and pragmatic coding elements in languages. Some of the latter are based on repetition and rhythm patterns, others on stress/prosody, order of elements (as we also see in the genome). Others (morphology, closed-class forms) derive from the lexicon, utilize segments instead of prosody, etc., and end up competing with the latter for influence.

But the prosodic/rhythmic/order parts of the system are also capable of generating new sequences with segments (consonants, vowels, etc.)- and when they do so, these have an iconic relationship with their meanings (sound symbolism), that utilizes the internal geometry and symmetry of the phonological system itself to pattern the meanings (diagrammatical iconicity).

What goes on in the genome/proteome is largely parallel- in organization, in function, and in evolution. Each morphosyntactic type of language associates with a type of genome. Lots more. This isn't the place to expand on all this though.

However, this kind of parallelism with function, loss of function and refunctionalization, cycles, types, shift from iconicity to symbolicity to indexicality and back again can arise without any need for an outside intelligence pushing things along. There is even evidence that the periodic table has been part of a similar evolution, given that the properties of elements (even basic electronic configurations) can't be read right off the chart. Outer context is involved too.

Jess Tauber

Intelligent Designer said:

Malchus said: I continue to pray for your redemption, but I fear hell awaits you on your present course.

This is one reason why I am not a Christian.

fnxtr said: Check and mate. Well played, eric.

eric said:

Curious said: Can you please provide a test or experiment to verify whether a sequence is in actual fact "junk DNA".

Did you read the original post? The authors experimentally showed that most of it is not transcribed. Creationists should pay particular attention to the Timmer quote too (that these sequences are not evolutionarily conserved). These are areas with a lot of mutation. The standard creationist line is that mutations only reduce function; but now you're stuck between a rock and a hard place, aren't you? The creationist model on one hand demands these regions have a function, yet on the other it demands that the large amount of mutation in these regions reduce its function. Its self-contradictory.

Nobody in the world calls me "Paul Zachary" or "Zachary". It's pretty much a dead giveaway that you're being some kind of pompous smartass. So I'm sorry, I don't believe your question is at all sincere, and you can go jump in a lake.

After you've dried out, though, you could pay attention to the scientific literature and the other people here, and look into comparative and functional studies. Junk is the stuff that doesn't do anything if you remove it and that shows relatively little conservation.

And that's more of an answer than a pretentious ass deserves.

Jess Tauber said: However, this kind of parallelism with function, loss of function and refunctionalization, cycles, types, shift from iconicity to symbolicity to indexicality and back again can arise without any need for an outside intelligence pushing things along. There is even evidence that the periodic table has been part of a similar evolution, given that the properties of elements (even basic electronic configurations) can't be read right off the chart. Outer context is involved too.

PZ Myers said: Nobody in the world calls me "Paul Zachary" or "Zachary". It's pretty much a dead giveaway that you're being some kind of pompous smartass. So I'm sorry, I don't believe your question is at all sincere, and you can go jump in a lake. After you've dried out, though, you could pay attention to the scientific literature and the other people here, and look into comparative and functional studies. Junk is the stuff that doesn't do anything if you remove it and that shows relatively little conservation. And that's more of an answer than a pretentious ass deserves.

Hey, I think Mr. Curious has an interesting point. Junk DNA is as junk DNA does. HeLa has a bit more junk than the human genome does, though it hasn't had much time to show the diagnostic markings (i.e. neutral evolution, lack of expression, etc.). We all know the primate GULO gene is junk DNA; HeLa just contains a great number of genes that are useless, most of them never expressed, in its environment.

I'm not sure what his point was intended to be -- probably something stupid but snarky -- but that's a nice thought.

Curious said: [snip] Am I to celebrate all of a sudden and claim I have found myself some junk DNA? I await your answer Paul. Thanks.

Ian Musgrave said: No need for celebration, your study will just join a long line of such studies. For example see: Deletion of ultraconserved elements yields viable mice. Ahituv N, Zhu Y, Visel A, Holt A, Afzal V, Pennacchio LA, Rubin EM. PLoS Biol. 2007 Sep;5(9):e234.

John Harshman said:

Ian Musgrave said: Deletion of ultraconserved elements yields viable mice. Ahituv N, Zhu Y, Visel A, Holt A, Afzal V, Pennacchio LA, Rubin EM. PLoS Biol. 2007 Sep;5(9):e234.

That, at least is a problem for the idea of finding junk DNA by deletion. Ultraconserved elements can't be junk, yet their excision apparently has no phenotypic, much less selective, consequences. But still, the sequences are conserved exactly throughout mammals. Either that conservation is maintained by selection or by some unknown and currently unimagined process. I pick selection. And that selection doesn't have to be extremely strong, just with a very specific target.

These results, while not inclusive of all the possible phenotypic impact of the deleted sequences, indicate that extreme sequence constraint does not necessarily reflect crucial functions required for viability.

Joe Felsenstein said:

John Harshman said: And that selection doesn't have to be extremely strong, just with a very specific target.

... which is the point. The test of whether mice with the ultraconserved sequences removed are “viable” does not prove that the deletions are not under selection.

It seems my initial celebration for finding junk DNA would have been premature. However I would like to hear from Zachary.

So let's ramp up the experiment a little.
HeLa cells have been used in many labs. Now let's say I collect HeLa cells from 10 different laboratories from all over the world. Not all of them will be genetically identical (in fact none of them will be) of course since they will have had different selection pressures and different random variation events (mutations, mitotic slippage etc.).

I do a few experiments:
Cell viability and cell growth tests,
Cell cycle analysis,
Autophagic and apoptotic activity,
Gene expression analysis (microarrays),
Protein expression analysis (protein arrays),
ROS production analysis,
Mitochondrial membrane potential analysis,
A few morphological studies (TEM, SEM, live cell imaging etc.),
Sequencing and karyotyping of the genomes.

After all this work (phew, I can see a PhD for a student from this), I hypothetically find that 3 of the cell lines from the different labs are very similar in all the parameters except for the sequence difference.
In other words, the 3 cell lines mentioned have similar cell viability, cell growth, cell cycle, autophagic, apoptotic, gene and protein expression analysis, ROS production, mitochondrial membrane potential, morphological and karyotype profiles, but they vary considerably in certain regions of the genome, say for example on chromosome 4.

I discover that these regions are non-coding and removal of these sequences has no effect on the abovementioned parameters.

Am I to celebrate all of a sudden (now) and claim I have found myself some junk DNA?

Curious said: It seems my initial celebration for finding junk DNA would have been premature. However I would like to hear from Zachary. So let's ramp up the experiment a little. HeLa cells have been used in many labs. Now let's say I collect HeLa cells from 10 different laboratories from all over the world. Not all of them will be genetically identical (in fact none of them will be) of course since they will have had different selection pressures and different random variation events (mutations, mitotic slippage etc.). I do a few experiments: Cell viability and cell growth tests, Cell cycle analysis, Autophagic and apoptotic activity, Gene expression analysis (microarrays), Protein expression analysis (protein arrays), ROS production analysis, Mitochondrial membrane potential analysis, A few morphological studies (TEM, SEM, live cell imaging etc.), Sequencing and karyotyping of the genomes. After all this work (phew, I can see a PhD for a student from this), I hypothetically find that 3 of the cell lines from the different labs are very similar in all the parameters except for the sequence difference. In other words, the 3 cell lines mentioned have similar cell viability, cell growth, cell cycle, autophagic, apoptotic, gene and protein expression analysis, ROS production, mitochondrial membrane potential, morphological and karyotype profiles, but they vary considerably in certain regions of the genome, say for example on chromosome 4. I discover that these regions are non-coding and removal of these sequences has no effect on the abovementioned parameters. Am I to celebrate all of a sudden (now) and claim I have found myself some junk DNA?

Malchus, would you claim you have found junk DNA from the above example?

Btw, the author's name is Paul Zachary Myers, and I am still awaiting a reply from him. If he does not want to reply, it is understandable. Calling a person by their name can be a traumatic experience I guess. My apologies.

Curious said: Malchus, would you claim you have found junk DNA from the above example? Btw, the author's name is Paul Zachary Myers, and I am still awaiting a reply from him. If he does not want to reply, it is understandable. Calling a person by their name can be a traumatic experience I guess. My apologies.

By the way, if you are unable to understand that you have already been answered, I would suggest you look to the prior posts on this and the preceding page.

Curious said: Malchus, would you claim you have found junk DNA from the above example? Btw, the author's name is Paul Zachary Myers, and I am still awaiting a reply from him. If he does not want to reply, it is understandable. Calling a person by their name can be a traumatic experience I guess. My apologies.

Malchus said: By the way, if you are unable to understand that you have already been answered, I would suggest you look to the prior posts on this and the preceding page.

Professor Myers is a full professor of an esteemed University, you are asking him to respond in his professional capacity, and you plainly do not know him personally. It is grossly rude of you to call him by his middle name. He's "Professor Myers" to you.

The response of a gentleman to gross rudeness is to ignore the person offering it.

Malchus said: And the answer, of course, is quite possibly. How are you defining "junk" DNA?

Dave Luckett said: Professor Myers is a full professor of an esteemed University, you are asking him to respond in his professional capacity, and you plainly do not know him personally. It is grossly rude of you to call him by his middle name. He's "Professor Myers" to you. The response of a gentleman to gross rudeness is to ignore the person offering it.

In other words, you demand of him behaviour that you do not display yourself. Thus, you have passed from "boor" to "hypocrite" in one easy thrust of the spade. But by all means, keep on digging.

Dave Luckett.

I do not pretend to be behaving like a Professor and a gentleman, you are of course suggesting he is a gentleman and he is afterall a Professor. If he is a gentleman, then I suggest he behaves like one and ignore the non-gentleman-like behaviour of others and stick to the topic at hand.

Dave, now could you be like a gentleman and also at least try and give an answer to the question. I fear these squabbles you are trying to fuel are not going to lead to anything meaningful.

I'll ask you again:

In this example (http://pandasthumb.org/archives/2010/05/junk-dna-is-sti.html#comment-218018), can I claim to have found junk DNA? If not, how ould you improve the experiment to verify the presence of junk DNA?
Thanks.

As I remarked, he is displaying the behaviour of a gentleman by ignoring you. As do I, henceforth.

Curious said:

Malchus said: And the answer, of course, is quite possibly. How are you defining "junk" DNA?

Malchus, I do not know exactly how to define junk DNA so that it is not a meaningless and vacuous term, nevermind test for it. Hence my example and question.

Dave Lovell said:

Curious said:

Malchus said: And the answer, of course, is quite possibly. How are you defining "junk" DNA?

Malchus, I do not know exactly how to define junk DNA so that it is not a meaningless and vacuous term, nevermind test for it. Hence my example and question.

But you still say "A simple yes or no is fine". What possible merit is there in a yes or no answer to anything other than an unambiguous question?

Dave Lovell said:

Curious said:

Malchus said: And the answer, of course, is quite possibly. How are you defining "junk" DNA?

Malchus, I do not know exactly how to define junk DNA so that it is not a meaningless and vacuous term, nevermind test for it. Hence my example and question.

But you still say "A simple yes or no is fine". What possible merit is there in a yes or no answer to anything other than an unambiguous question?

Dave Lovell said:

Curious said:

Malchus said: And the answer, of course, is quite possibly. How are you defining "junk" DNA?

Malchus, I do not know exactly how to define junk DNA so that it is not a meaningless and vacuous term, nevermind test for it. Hence my example and question.

But you still say "A simple yes or no is fine". What possible merit is there in a yes or no answer to anything other than an unambiguous question?

It seems to experimentally verify junk DNA is a meaningless task and not worth pursuing since the concept itself is scientifically vacuous. Sort of like ID.

No-one's got a gun to your head, Curious. You are free not to pursue this line of inquiry any farther, since you clearly think it unimportant.

See ya.

Curious said: It seems to experimentally verify junk DNA is a meaningless task and not worth pursuing since the concept itself is scientifically vacuous. Sort of like ID.

Curious said: It seems to experimentally verify junk DNA is a meaningless task and not worth pursuing since the concept itself is scientifically vacuous. Sort of like ID.

Junk DNA as a colloquialism seems to merely apply to DNA that is a provisionally labeled for sequences of DNA for which no function has been identified.

And of course, I will leave it to you to try and figure out a proper definition of "function" as it applies to the colloquialism... junk DNA.

It however does not imply that junk DNA is functionless since that would merely be an argument from ignorence...like ID. Besides, I don't think a single person will argue that sequences of DNA for which no function has been identified will never even have the potential to be functional given random variation and selection. That is just another argument from ignorance...like ID.

Junk DNA as a colloquialism seems to merely apply to DNA that is a provisionally labeled for sequences of DNA for which no function has been identified.

Jesse said:

Junk DNA as a colloquialism seems to merely apply to DNA that is a provisionally labeled for sequences of DNA for which no function has been identified.

Or, junk DNA is DNA that can be removed with no ill effects. Because it's not necessary. I'm just sayin'

curious said: Junk DNA as a colloquialism seems to merely apply to DNA that is a provisionally labeled for sequences of DNA for which no function has been identified.

Curious said:

Jesse said:

Junk DNA as a colloquialism seems to merely apply to DNA that is a provisionally labeled for sequences of DNA for which no function has been identified.

Or, junk DNA is DNA that can be removed with no ill effects. Because it's not necessary. I'm just sayin'

Necessary for what? Arguments from ignorance like these are not going to convince many people honestly... well perhaps IDers.

eric said: As other folks have mentioned, expanding the genome with otherwise useless filler reduces the chance that cosmic radiation will cause an error in a developmentally important part of the genome.

Curious -

You are certainly wasting a great deal of time on stupid semantic games.

It is common to refer to non-coding DNA that does not show the type of sequence preservation we would expect, if sequence changes were selected against, as "junk DNA".

This usage is conventional rather than technical. You don't have to call anything "junk" DNA if you don't want to.

You appear to worship a god who encourages obnoxious, confrontational behavior, or at least, adhere to an ethical system that does so. You appear to feel that your god or ethical system is somehow threatened if some segments of DNA in eukaryotic cells have little or no "function". That is entirely your own self-created personal problem.

In many cases, deletions of large amounts of this DNA from cells appears to have no obvious strong impact on the phenotype.

I and others among those who respect and basically agree with PZ Meyers have pointed out, repeatedly, that subtle impacts of deleting such DNA have also been observed, in some cases. The origins and impact of the diverse varieties of non-coding DNA remain, to some of us, an interesting area of study.

Unfortunately, at least based on your posts here, you are not qualified to meaningfully contribute to this area of study. Your emotional biases are too severe to allow you to function in a relevant way.

1) You are obsessed with the trivial semantics of the term "junk" DNA rather than interested in actual results and observations.

2) You claim an interest in the area, but are so ignorant of prior research that you don't even know the things that a google search would reveal. Failure to familiarize oneself with the work which has already been done is a non-starter in scientific research.

3) You are unable to discuss the evidence in a civil, collegial way with those who are knowledgeable in the field.

John Harshman said:

eric said: As other folks have mentioned, expanding the genome with otherwise useless filler reduces the chance that cosmic radiation will cause an error in a developmentally important part of the genome.

Why would that be? Mutation rates are generally considered to be probabilities per site. Expanding the genome shouldn't change the rate per site at all, and so shouldn't affect the chance of a mutation in any particular spot.

Dave Lovell said: But if this is a significant mechanism, would it not suggest that the proportion of junk DNA should tend to be lower in deep sea creatures shielded from cosmic radiation?

But does creationism necessarily logically require the absence of detritus?

But then again, theism in general doesn't logically require the absence of evolution, either - the claimed inconsistency there is because of assumptions about the details of a particular version of theism, not the basic concept.

Eric -

Yes, ultimately, that is the point.

I do have a minor problem with anthropomorphic, subjective terms like "junk", or even "detritus". I even have a problem with semantic issues revolving around the word "function". I have a problem with making statements that go (even if only slightly) beyond the evidence.

But at the end of the day, non-coding, not-directly-regulatory DNA just isn't a problem for the theory of evolution, no matter what. And it never has been seen as one.

Some people have invented a god or philosophy whose existence or validity is incompatible with the existence of non-coding DNA.

Well, that's just tough for them. There is a lot of non-coding DNA. Their particular god or philosophy must be false (and usually is for many other reasons as well). Their denial often takes the form of ludicrous, uninformed, insultingly ignorant "conjecturing" about "junk" DNA. But the problem is entirely theirs.

Henry J said: But does creationism necessarily logically require the absence of detritus?

But then again, theism in general doesn't logically require the absence of evolution, either - the claimed inconsistency there is because of assumptions about the details of a particular version of theism, not the basic concept.

harold said: But at the end of the day, non-coding, not-directly-regulatory DNA just isn't a problem for the theory of evolution, no matter what. And it never has been seen as one.

Mike Elzinga said: I think with ID/creationists, it is a knee-jerk, Pavlovian response to make up crap on the spot in order to look like they are putting forward fatal counter-arguments to “evilutionist” dogma.

MrG said: The really odd thing is that, as a rule, (creationists) honestly think their arguments hold water.

John Harshman said:

eric said: As other folks have mentioned, expanding the genome with otherwise useless filler reduces the chance that cosmic radiation will cause an error in a developmentally important part of the genome.

I don't know, seems to me that expanding the genome simply increases the chance of mutation; the more genetic material, the greater the chance of a hit by a cosmic ray. But there are other considerations, is the genome tightly wound.. that would affect its cross-section and the chance of a hit and to what extent the tree trunks can protect the soldiers. Why would that be? Mutation rates are generally considered to be probabilities per site. Expanding the genome shouldn't change the rate per site at all, and so shouldn't affect the chance of a mutation in any particular spot.

Dave Lovell said:

John Harshman said:

eric said: As other folks have mentioned, expanding the genome with otherwise useless filler reduces the chance that cosmic radiation will cause an error in a developmentally important part of the genome.

Why would that be? Mutation rates are generally considered to be probabilities per site. Expanding the genome shouldn't change the rate per site at all, and so shouldn't affect the chance of a mutation in any particular spot.

Not if almost all cosmic rays pass through a cell without interaction with its DNA. It's like trying to shoot soldiers in a forest with a randomly aimed machine gun. The higher the ratio of tree trunks to men, the more bullets are that are neutralised by trees. But if this is a significant mechanism, would it not suggest that the proportion of junk DNA should tend to be lower in deep sea creatures shielded from cosmic radiation?

Stuart Weinstein said: Weird... my reply was truncated.. I was saying that there is some dependence on how tightly wound the genome is. That will effect the cross-section area and how well the tree trunks can protect the soldiers..

All expanding the genome does is increase the chance of mutation.

Does. Not. Work.

There is no arbitrary mechanism that says the genome only gets X number of mutations per replication event. The rate is per nucleotide.

If you have an error rate of 10 in 52 for your deck of cards, the original deck will have, on average, 10 errors per year. Your inflated deck of 520 cards will have, on average, 100 errors per year, 10% of which will fall on the original good cards, or 10 errors that matter. Same number.

Dave Lovell said: Not if almost all cosmic rays pass through a cell without interaction with its DNA. It's like trying to shoot soldiers in a forest with a randomly aimed machine gun. The higher the ratio of tree trunks to men, the more bullets are that are neutralised by trees

Jesse said:

Joe Felsenstein said: Interesting, a good summary. Opponents of evolutionary biology are always saying that “Intelligent Design predicts that there is no junk DNA”. They also say that ID is not religion but a straightforward scientific theory. Now I can think of theological arguments against the existence of junk DNA (along the lines of “No self-respecting Deity would ...”). But if we rule out that theological argument, exactly where in ID do this supposed “prediction” come from? I don't recall anything in the writings of Dembski or Behe that makes any such prediction. Does anyone have a non-theology source for it?

Lemme pull an ID bait and switch on you here simply to answer your question: "...along the lines of “No self-respecting Deity Intelligent Designer would..." This only has any meaning if we know something about the Intelligent Designer. Since, for the ID folks, it is already known a priori that the designer is God and we are made in his image, it all fits in nicely with their little framework.

Ben Vallejo said:

Jesse said:

Joe Felsenstein said: Interesting, a good summary. Opponents of evolutionary biology are always saying that “Intelligent Design predicts that there is no junk DNA”. They also say that ID is not religion but a straightforward scientific theory. Now I can think of theological arguments against the existence of junk DNA (along the lines of “No self-respecting Deity would ...”). But if we rule out that theological argument, exactly where in ID do this supposed “prediction” come from? I don't recall anything in the writings of Dembski or Behe that makes any such prediction. Does anyone have a non-theology source for it?

Lemme pull an ID bait and switch on you here simply to answer your question: "...along the lines of “No self-respecting Deity Intelligent Designer would..." This only has any meaning if we know something about the Intelligent Designer. Since, for the ID folks, it is already known a priori that the designer is God and we are made in his image, it all fits in nicely with their little framework.

Ken Miller said in 1994 that DNA is filled with junk left over from naturalistic, random evolution: …the designer made serious errors, wasting millions of bases of DNA on a blueprint full of junk and scribbles. Michael Behe said in 2002 that DNA isn’t as junky some people think, because of the evidence: As a public skeptic of the ability of Darwinian processes to account for complex cellular systems and a proponent of the hypothesis of intelligent design, (1) I often encounter a rebuttal that can be paraphrased as “no designer would have done it that way.” …
If at least some pseudogenes have unsuspected functions, however, might not other biological features that strike us as odd also have functions we have not yet discovered? Might even the backwards wiring of the vertebrate eye serve some useful purpose?
….
 As far back as 1994, pro-ID scientist and Discovery Institute fellow Forrest Mims had warned in a letter to Science[1] against assuming that 'junk' DNA was 'useless.'" Science wouldn't print Mims' letter, but soon thereafter, in 1998, leading ID theorist William Dembski repeated this sentiment in First Things: [Intelligent] design is not a science stopper. Indeed, design can foster inquiry where traditional evolutionary approaches obstruct it. Consider the term "junk DNA." Implicit in this term is the view that because the genome of an organism has been cobbled together through a long, undirected evolutionary process, the genome is a patchwork of which only limited portions are essential to the organism. Thus on an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function. And indeed, the most recent findings suggest that designating DNA as "junk" merely cloaks our current lack of knowledge about function. For instance, in a recent issue of the Journal of Theoretical Biology, John Bodnar describes how "non-coding DNA in eukaryotic genomes encodes a language which programs organismal growth and development." Design encourages scientists to look for function where evolution discourages it. (William Dembski, "Intelligent Science and Design," First Things, Vol. 86:21-27 (October 1998)) In 2002, Dr. Richard Sternberg surveyed the literature and found extensive evidence for function of certain types of junk-DNA and argued that "neo-Darwinian 'narratives' have been the primary obstacle to elucidating the effects of these enigmatic components of chromosomes."[1] Sternberg concluded that "the selfish DNA narrative and allied frameworks must join the other ‘icons’ of neo-Darwinian evolutionary theory that, despite their variance with empirical evidence, nevertheless persist in the literature.”[2] Then in 2004, pro-ID molecular biologist Jonathan Wells argued that "The fact that ‘junk DNA’ is not junk has emerged not because of evolutionary theory but in spite of it. On the other hand, people asking research questions in an ID framework would presumably have been looking for the functions of non-coding regions of DNA all along, and we might now know considerably more about them."[4] I also have the article from nature concerning the Junk DNA paradigm, and it disputes the term Junk DNA based on current data. There seems to be a lot of denial and a back lash at anyone who disputes orthodox Darwinian inspired thought, even at the non religious Encode project.

Ben, first of all, quoting Dr. Dr. D and The Pastor Dave of ID are not going to gain you any traction here.

Second, did you even read the original post?

Ben Vallejo said:(emphasis added) Junk DNA, a term that was introduced in 1972 by Susumu Ohno,[6] is a provisional label for the portions of a genome sequence for which no discernible function has been identified. According to a 1980 review in Nature by Leslie Orgel and Francis Crick, junk DNA has "little specificity and conveys little or no selective advantage to the organism".[7] The term is currently, however, a somewhat outdated concept, being used mainly in popular science and in a colloquial way in scientific publications, and may have slowed research into the biological functions of noncoding DNA.[8] Several lines of evidence indicate that many "junk DNA" sequences have likely but unidentified functional activity, and other sequences may have had functions in the past.[9]

As I recall, the presence of a lot of junk (i.e., unused) DNA wasn't predicted prior to its discovery, nor is it necessarily entailed by the current theory.

Also, I don't see any reason why "life was deliberately engineered" would necessarily imply the absence of unused DNA, anyway. So if either its presence or absence is consistent with either ToE or "IDC", then why are anti-ToE advocates fussing about this particular detail?

I don't get it.

Henry J

Creationists have campaigned for Devolution. That is, decay and disintegration of the biosphere, really, universe itself.

Genome contains bewildering amount of retroviral rubbish, maybe even 1/10 of it. Estimates for the intergenic transcripts are 4-20% of all genes. Spliceisoforms have steadily increased to an estimate of over 80% of the genes. I think these structural degenerations may well end up contributing to disease, pathology and death. Let us remember that even the poisons aka viruses are not poisonous until they lyse the cells. Only now have we begun vaccinating against parvo virus etc. that may be causative agents to poking DM type I even.

http://www.helsinki.fi/~pjojala/Haeckelianlegacy_ABC5.pdf

Creationists have campaigned for Devolution. That is, decay and disintegration of the biosphere, really, universe itself.

Henry J said: Also, I don't see any reason why "life was deliberately engineered" would necessarily imply the absence of unused DNA, anyway.

Pauli Ojala said: Creationists have campaigned for Devolution.

We lost our tails

Evolving up

From little snails

I say it's all

Just wind in sails...

fnxtr said: They tell us that

We lost our tails

Evolving up

There's probably a fetish website for that, too.

Ian Musgrave said: There are several lines of evidence that most of the DNA in humans and other organisms is junk. ... c) The majority of non-coding DNA accumulates mutations at the maximal rate. There is no sequence conservation. If these things had a role as, say regulatory sequences, then they would be conserved.

Inventing a new pseudoscientific term for a phenomenon which has no empirical evidence for its existence except for a brief mention on your dismally malinformative blog is not a rationale, Mr Stimpson.

See the "TV Tropes" website entry on "Applied Phlebotinum" for insight:

http://tvtropes.org/pmwiki/pmwiki.php/Main/AppliedPhlebotinum

Intelligent Designer said: But let's say that we know some DNA accumulates mutations at the maximal rate. We can't conclude that the DNA is junk. ...I can think of at least two other possibilities: 1) The DNA only affects the longevity of the life form. For example it may be part of the immune system or it may support a redundant or non-vital system.

2) It may not be expressed in the current life form and may in fact take several generations to be expressed. Its purpose may only be for adaptive capacitance.

PZ Myers said: Inventing a new pseudoscientific term for a phenomenon which has no empirical evidence for its existence except for a brief mention on your dismally malinformative blog is not a rationale, Mr Stimpson.

PZ Myers said: Inventing a new pseudoscientific term for a phenomenon which has no empirical evidence for its existence except for a brief mention on your dismally malinformative blog is not a rationale, Mr Stimpson.

Intelligent Designer said:

PZ Myers said: Inventing a new pseudoscientific term for a phenomenon which has no empirical evidence for its existence except for a brief mention on your dismally malinformative blog is not a rationale, Mr Stimpson.

I didn't exactly invent the term. I just choose more neutral term for term "evolutionary capacitance" used extensively by Jerry Coyne in "Why Evolution is True". You will also find that Wikipedia, perhaps incorrectly, states that "evolutionary capacitance" is a biological theory. Jerry Coyne presents it as evidence for evolution. I think it is evidence for intelligent design. Also your own blog presents evidence for the hypothesis here.

SWT said: "Evolutionary capacitance" ... you keep using that term. I do not think it means what you think it means. You might want to check out the original paper by Bergman and Siegel where it's defined.

Intelligent Designer said:

SWT said: "Evolutionary capacitance" ... you keep using that term. I do not think it means what you think it means. You might want to check out the original paper by Bergman and Siegel where it's defined.

The paper you sited provides more specific details but I don't see anything in it contrary to what I have stated.

I'm late to this party, but I've been puzzled at the apparent controversy over so-called Junk DNA.

Imagine a world in which the evolutionary hypothesis is true. As evolution progresses, one would *expect* the process to be messy and leave behind nonfunctional pieces. Nobody would expect the process of evolution to 'clean up' after itself. Would we? Unless there were an evolutionary advantage to doing so, and it seems more likely there would be lots of 'junk' lying around that had a purpose when it started and no long does.

A billion years of evolution, a billion years of evolutionary trash left behind - not only is that not surprising, it would be mighty surprising if it were any other way. It seems to me inevitable that some features of the genome will be nonfunctional left-behinds. So what's the big deal?

That's exactly right - as I understand it, there is no big deal scientifically, and you're probably right that there would be if there wasn't a lot of junk. (Although I do recall that the prevalence of junk wasn't predicted ahead of time.)