"The case for junk DNA"

[rwatts]

It's worth expanding on one of the points made briefly in the article.

Genetic fingerprinting works by measuring the number of copies a person has of each of several repeated DNA sequences. The number of repetitions of each of these sequences varies widely among individuals, and there are trillions of possible combinations of copy numbers, making the chance that any two random people have the same combination very small. Since the DNA in these repeated sequences can vary in length without any apparent effect, it's clear that the repetitions beyond the minimum number found for each of these sequences are unnecessary. Or, to put it another way, if there was no 'junk' DNA, genetic fingerprinting would not work. Since it does work, there is 'junk' DNA.

Roy

I thought the "Onion test" was a beauty as well.

[rwatts]

Yes, an insignificant portion of DNA may become "junk" due to deleterious mutation(s) but, ....

Getting ready for the backpedal?

... overall, there is no "junk" in the DNA due to an Evolutionary history.

But there would be. Once a gene turns to junk you have a modification which gets passed on by common descent. (Common descent with modification.).

It would become part of a phylogenetic signal, which could be used to construct trees illustrating degrees of relatedness.

[rwatts]

That it does 'nothing' is overreaching.

A lot of what was considered junk, does appear to get transcribed and even translated.

However, they think this is still junk in the sense that it fails to produce useful protein. With the stuff that gets transcribed but not translated, it gets broken down. The stuff that goes to translation is open to selection. There is a possibility that new genes evolve this way:-

The Continuing Evolution of Genes

Proto-genes and de novo gene birth

[TheLurch]

I'm on travel now but I can think of no better source to give you than The Myth of Junk DNA by J. Wells. Any reasonable, fair-minded person reading that book would immediately and forevermore abandon the notion of DNA being "junk" in whole or in part.

Well, knowing the book and having talked with Wells a number of times, the conclusion i reach is that Wells himself is not a reasonable, fair-minded person. He makes fundamental errors about biology when discussing junk DNA, and all indications are that he's doing so in order to reach the conclusions that he desires.

Also, and quickly, I'm likely nowhere near your level of expertise in molecular and cell biology. I'm more versed in information theory and it is on that basis that I've determined that the notion of "junk DNA" is unsupportable. Specifically, you are aware, I presume, of the multiple codes in the DNA - also known as poly-functional DNA. Trifanov identified no fewer than twelve separate codes in DNA (1-2). In a paper that I co-authored (3) we listed sixteen codes with others possible.

That's completely orthogonal to junk DNA. The "multiple codes" papers are about areas that encode proteins. Nobody considers those junk.

So, again, when your travels allow, i'd like to hear some of the evidence you feel has supported your position.

[Jorge]

It looks to me as if you did not read the paper Jorge. It's reasonably readable for laymen like you and me.

They provide good reasons for thinking there is still a lot of junk.

Just returned from dinner having left TWeb "on" ...

As always, you speak and judge without proper basis. Just what part of the paper do you think I haven't read (or understood)? I'll summarize for you what I picked up in the paper:

The authors (Palazzo and Gregory - P&G) have either forgotten their history or, in typical Evolutionist less-than-honest fashion, are giving us an 'Revised Evolutionist Version' in which the Evolutionists don't have egg on their face regarding all of the things that they believed, claimed and published in prestigious scientific journals about "junk DNA" in years past. The 'proof' of this is simple: why would so much effort have been spent by so many people to demonstrate -based on scientific observations - that the "junk DNA" claim is wrong if that claim wasn't there to begin with? It WAS there - I witnessed it and so did most of you people here on TWeb (you're old enough). You were there when "junk DNA" was loudly being trumpeted as "proof" of Evolution. Heck, O-Mudd repeats as much in an earlier post here. Now it appears that your recollections have 'morphed' into the REV (Revised Evolutionist Version).

I agree that P&G state many things in the paper that are scientifically true - I do not dispute that. What I am saying is that much in the paper is revised history, backpedaling and hindsight. Just another instance of the ethics that Evolutionists often employ. For example:



Only a person that has forgotten how it was 15-25 years ago (i.e., what was being said, taught and published) could write those words. I distinctly remember titles such as "JUNK DNA - Evolutionary Remnants" in which the authors boldly spoke of "junk DNA" as all but "proof" of an Evolutionary history. Now it's, "Oh, we knew it all along ... nobody said that ... repugnant". Yeah, rrrrrrright.

Jorge

[rwatts]

The authors (Palazzo and Gregory - P&G) have either forgotten their history ...

Unlikely.

A lot of their paper referred back to the history of the idea of "junk DNA". They reference associated material.

... or, in typical Evolutionist less-than-honest fashion, are giving us an 'Revised Evolutionist Version' in which the Evolutionists don't have egg on their face regarding all of the things that they believed, claimed and published in prestigious scientific journals about "junk DNA" in years past.

Again that makes no sense, given that this junk/no junk argument as mostly been one between evolutionists. After all, unlike most of the creation scientists, evolutionists do actual research. So naturally, they would find evidence for junk DNA which would spark the skepticism of other evolutionists, and various evolutionists, as science progresses, would find evidence for so called junk DNA having actual functionality.

The 'proof' of this is simple: why would so much effort have been spent by so many people to demonstrate -based on scientific observations - that the "junk DNA" claim is wrong if that claim wasn't there to begin with? It WAS there - I witnessed it and so did most of you people here on TWeb (you're old enough). You were there when "junk DNA" was loudly being trumpeted as "proof" of Evolution. Heck, O-Mudd repeats as much in an earlier post here. Now it appears that your recollections have 'morphed' into the REV (Revised Evolutionist Version).

???

But the authors of that paper you claim to have read, show why the idea of junk DNA is still very relevant. And nothing has morphed. These authors are simply pointing out that too much is being made of the no junk DNA claim. They take a swipe at ENCODE for its bloated claims about 80% or more being functional.

Are you sure you actually read it Jorge?

I agree that P&G state many things in the paper that are scientifically true - I do not dispute that. What I am saying is that much in the paper is revised history, backpedaling and hindsight. Just another instance of the ethics that Evolutionists often employ. For example:



Only a person that has forgotten how it was 15-25 years ago (i.e., what was being said, taught and published) could write those words. I distinctly remember titles such as "JUNK DNA - Evolutionary Remnants" in which the authors boldly spoke of "junk DNA" as all but "proof" of an Evolutionary history. Now it's, "Oh, we knew it all along ... nobody said that ... repugnant". Yeah, rrrrrrright.

Jorge

But Jorge, they cite references to researchers (evolutionists) who were against the notion of junk-DNA. That is, it was not universally accepted. Nevertheless, as these authors point out, there is good scientific reason to maintain that it does exist, in vast quantities. They point out that the no junk DNA claim does not have a good pedigree. The evidence continues to weight against such a claim.

So, are you able to address that evidence?

[Jorge]

Well, knowing the book and having talked with Wells a number of times, the conclusion i reach is that Wells himself is not a reasonable, fair-minded person. He makes fundamental errors about biology when discussing junk DNA, and all indications are that he's doing so in order to reach the conclusions that he desires.

Okay ... that's interesting. I myself have read the book and could not find anything like what you say. Perhaps it's because I do not have a PhD in genetics and cell biology. Oh well ...

That's completely orthogonal to junk DNA. The "multiple codes" papers are about areas that encode proteins. Nobody considers those junk.

Nope - you missed the point - in fact, several points. First, it is not known exactly how many codes there are in all. The sixteen that we listed in our paper are just the ones that we have been able to identify. It would be illogical to assume that we have identified all of them. It is certainly possible (and likely) that other codes operate with noncoding portions of the DNA and/or that codes that operate within the coding portion of the DNA make use of noncoding portions (see next) . Second, we certainly don't know everything (in most cases anything) about how those codes work. It may well be that, like a subroutine in a computer program, they branch off into other parts of the DNA (coding or noncoding).

In any event, it is well beyond the observable facts to dogmatically claim that "junk DNA" is truly "junk" as certain Evolutionists do. They are merely speaking from ignorance.
One thing is indisputable: if most of the genome truly is "junk DNA" then that would support Evolutionism. If there is a miniscule, insignificant or no "junk DNA" in the genome then that would not support Evolutionism. In other words, there is undoubtedly an ideological motivation towards promoting the notion of junk DNA. I'll let you draw your own conclusions from that.

So, again, when your travels allow, i'd like to hear some of the evidence you feel has supported your position.

In his book, Wells presents much of the evidence that you request - links, references, etc. are plentiful in his book. I referred you to that book. You have summarily dismissed it as if with a magic wand - POOF! If you did that to Wells, who does have equal academic standing with you, for me you won't even bother to pull out your magic wand. Anywho ... I get back home next week.

Jorge

[Jorge]

Unlikely.

A lot of their paper referred back to the history of the idea of "junk DNA". They reference associated material.



Again that makes no sense, given that this junk/no junk argument as mostly been one between evolutionists. After all, unlike most of the creation scientists, evolutionists do actual research. So naturally, they would find evidence for junk DNA which would spark the skepticism of other evolutionists, and various evolutionists, as science progresses, would find evidence for so called junk DNA having actual functionality.



???

But the authors of that paper you claim to have read, show why the idea of junk DNA is still very relevant. And nothing has morphed. These authors are simply pointing out that too much is being made of the no junk DNA claim. They take a swipe at ENCODE for its bloated claims about 80% or more being functional.

Are you sure you actually read it Jorge?

But Jorge, they cite references to researchers (evolutionists) who were against the notion of junk-DNA. That is, it was not universally accepted. Nevertheless, as these authors point out, there is good scientific reason to maintain that it does exist, in vast quantities. They point out that the no junk DNA claim does not have a good pedigree. The evidence continues to weight against such a claim.

So, are you able to address that evidence?

If you also are going to make use of REV and deny that such Historical Revisionism is taking place then there's really not much more to say. I could, of course, (after returning home) spend hours or days of my time digging up article after article from the 1980's and 1990's in which the history as I state it is there in black and white for you to see but, no, I've been down that road before. After spending (wasting!) all that time you will merely pull something else out of your hat. Believe as you wish. I am sure that some of you here remember well enough but you'd be booted out of the Evolutionists-R-Us Club should you dare say anything.

jorge

[klaus54]

True. HOWEVER ...

You people are always bringing up the "God of the gaps" nonsense, saying that the "gaps are decreasing inversely with knowledge" (a stupid remark, but that's another story).

Well, okay, as more and more is observed/discovered, much of what was once believed (by the Evos) to not have significance/play a part is now known to be significant/play a part. Ergo, my claim IS falsifiable.

Spelling it out for you (as I know of your logic handicap) - if since the 1990's (when I made my prediction) the opposite would have been observed (i.e., NO function for the "junk" would have been observed/discovered) then I would have been falsified. Instead, what has been observed/discovered to date supports my claim (my claim is not proven, but certainly supported and most certainly not falsified). Furthermore, I predict that this trend will continue. If it doesn't then I stand falsified.


Pay the lady a buck and do try again, Roy - it's always amusing.

Jorge

Jorge,

What does any of your blathering have to do with "God of the Gaps"? GoG is BTW a fairly good explanation for Dembski's notion of "irreducible complexity." Something or other is too complicated so "the designer" musta done it.

Surely you agree. If not, why not?

K54

[TheLurch]

Okay ... that's interesting. I myself have read the book and could not find anything like what you say. Perhaps it's because I do not have a PhD in genetics and cell biology. Oh well ...

The problems are pretty fundamental. Wells implies that any non-coding sequence was considered junk. The concept of junk DNA originated in the 70s; Jacob and Monot got their Nobel for the discovery of non-coding regulatory DNA in 1965; the results clearly were significantly earlier than that. So, the concept of noncoding regulatory DNA was already firmly established before the junk DNA discussion even started.

This is pretty fundamental stuff; the Lac operon is in every basic biology text. I can't possibly imagine why Wells chose to pretend it wasn't known about in writing his book.

Nope - you missed the point - in fact, several points. First, it is not known exactly how many codes there are in all. The sixteen that we listed in our paper are just the ones that we have been able to identify. It would be illogical to assume that we have identified all of them. It is certainly possible (and likely) that other codes operate with noncoding portions of the DNA and/or that codes that operate within the coding portion of the DNA make use of noncoding portions (see next) .

Having gone through the list, it's very clear that the vast majority of that number are either part of or would need to function in immediate proximity to the coding portions of a gene. The only exceptions appear to be structural functions, like binding to the nuclear scaffold. If you look into these in detail, they're relatively uncommon and only a few hundred bases long. Therefore, they cannot account for more than a tiny fraction of the DNA in eukaryotic genomes that is not conserved across species.

In any event, it is well beyond the observable facts to dogmatically claim that "junk DNA" is truly "junk" as certain Evolutionists do.

I'd agree with this. The evidence is that a significant portion of most eukaryotic genomes are what has been termed junk DNA, but that's a tentative conclusion, subject to further revision.

One thing is indisputable: if most of the genome truly is "junk DNA" then that would support Evolutionism. If there is a miniscule, insignificant or no "junk DNA" in the genome then that would not support Evolutionism. In other words, there is undoubtedly an ideological motivation towards promoting the notion of junk DNA. I'll let you draw your own conclusions from that.

Where as this, i suspect, is wrong. My only doubt is focused on the term "evolutionism", which i'm not familiar with. Assuming it means "someone who accepts the evidence for evolution", then the statement is false.

The relative percentage of junk DNA, within an evolutionary model, depends on the strength of selective pressure and effective population size. Things like copy number variations are constantly adding non-functional DNA to the genome, which has a very small, but non-zero energetic cost. There can be strong selective pressure to minimize the genome - examples include things like bacteria, where the minimizing energy expenditures is strongly selected for, or the bladderwort, which lives in an environment that doesn't provide it with much of a chemical that's essential to DNA (Phosphorous, i think). A large effective population size ensures that deletions that get rid of non-essential DNA occur with a reasonable frequency. Combine the two, and you get an organism with a compact, largely junk-free genome through standard evolutionary processes.

In his book, Wells presents much of the evidence that you request - links, references, etc. are plentiful in his book. I referred you to that book. You have summarily dismissed it as if with a magic wand - POOF!

As described above, Wells does not reliably present science in his book. So, it's not a summary dismissal; more of a critical evaluation.

[rwatts]

If you also are going to make use of REV and deny that such Historical Revisionism is taking place then there's really not much more to say. I could, of course, (after returning home) spend hours or days of my time digging up article after article from the 1980's and 1990's in which the history as I state it is there in black and white for you to see but, no, I've been down that road before. After spending (wasting!) all that time you will merely pull something else out of your hat. Believe as you wish. I am sure that some of you here remember well enough but you'd be booted out of the Evolutionists-R-Us Club should you dare say anything.

jorge

http://www.genomicron.evolverzone.co...series/. Accessed 10 April 2014.

That last link is worth scrounging through.

However, this (your grumbling) is all somewhat irrelevant.

The point is, the authors of the paper I linked to in the OP are maintaining that the non coding DNA is likely to be mostly junk or have a large component of junk. That is, they are countering the perception that evidence points to the non-coding DNA being all functional or mostly functional. They are pointing out that the evidence does not support this idea.

You haven't read the paper at all, have you. I find it odd, but typical, that your only argument to date, is to cry "revisionism" when all these guys are doing is remphasizing orthodoxy. Supporting orthodoxy is hardly revisionism.

So, would you like to address the science behind their claims that orthodoxy is correct, namely that a lot, if not most DNA is junk? I think they make a good case. I really liked their "Onion test" section. Look at their figure 1. The star represents the size of the human genome. Now look at the spread of mammalian genomes and look at the spread for other organisms. If the human genome is mostly, if not all functional, then how do you explain* this graph in the context of organismal complexity and genome size?


* Irrelevant rants are not "explainations" in my world. In your world they might be, but not mine.

[Jorge]

The problems are pretty fundamental. Wells implies that any non-coding sequence was considered junk. The concept of junk DNA originated in the 70s; Jacob and Monot got their Nobel for the discovery of non-coding regulatory DNA in 1965; the results clearly were significantly earlier than that. So, the concept of noncoding regulatory DNA was already firmly established before the junk DNA discussion even started.

This is pretty fundamental stuff; the Lac operon is in every basic biology text. I can't possibly imagine why Wells chose to pretend it wasn't known about in writing his book.


Having gone through the list, it's very clear that the vast majority of that number are either part of or would need to function in immediate proximity to the coding portions of a gene. The only exceptions appear to be structural functions, like binding to the nuclear scaffold. If you look into these in detail, they're relatively uncommon and only a few hundred bases long. Therefore, they cannot account for more than a tiny fraction of the DNA in eukaryotic genomes that is not conserved across species.


I'd agree with this. The evidence is that a significant portion of most eukaryotic genomes are what has been termed junk DNA, but that's a tentative conclusion, subject to further revision.


Where as this, i suspect, is wrong. My only doubt is focused on the term "evolutionism", which i'm not familiar with. Assuming it means "someone who accepts the evidence for evolution", then the statement is false.

The relative percentage of junk DNA, within an evolutionary model, depends on the strength of selective pressure and effective population size. Things like copy number variations are constantly adding non-functional DNA to the genome, which has a very small, but non-zero energetic cost. There can be strong selective pressure to minimize the genome - examples include things like bacteria, where the minimizing energy expenditures is strongly selected for, or the bladderwort, which lives in an environment that doesn't provide it with much of a chemical that's essential to DNA (Phosphorous, i think). A large effective population size ensures that deletions that get rid of non-essential DNA occur with a reasonable frequency. Combine the two, and you get an organism with a compact, largely junk-free genome through standard evolutionary processes.


As described above, Wells does not reliably present science in his book. So, it's not a summary dismissal; more of a critical evaluation.

Okay, I'll have to be back home where I have Wells' book and can refute with evidence some of your claims here (e.g., if memory serves me, Well's is fully aware that just because it's non-coding does not make it "junk".)

You also say that, "Wells does not reliably present science in his book." I am always amazed at how anyone no toeing the Evolutionary line is immediately dismissed as a "non-scientist". Examples are legion: Dean Kenyon was considered one of the top scientists in his field UNTIL he went against the Materialistic Evolutionary Paradigm at which point he was downgraded into 'basically' a lab technician. Same story for Mike Behe - regarded as a top-level scientist UNTIL he published Darwin's Black Box after which he was 'magically' transformed into a "pseudo-scientist". Here you say that "Wells does not reliably present science ..." Let me hazard a wild guess : Wells opposes the Evolutionary Paradigm. Yup, that'll do it every time.

As for the term "Evolutionism" - odd that you aren't familiar with it given that you subscribe and practice it. Evolutionism, concisely stated, is simply the metaphysical stance that Evolution explains the entire spectrum of flora and fauna in existence today as well as every aspect of intra- and inter-species phenomena. Evolutionism, taken to its logical implications, must also account for the emergence of life itself (although this is adamantly denied by the practitioners of Evolutionism). In a nutshell, that is Evolutionism.

Anyway, I got'ta get going - next stop Chicago, IL. I'll consider this after I'm back home but I will confess that it won't be on my priority list.

Jorge

[JonF]

You also say that, "Wells does not reliably present science in his book." I am always amazed at how anyone no toeing the Evolutionary line is immediately dismissed as a "non-scientist"

We all see how you ducked the issue and tried to change the subject there.

[oxmixmudd]

If you also are going to make use of REV and deny that such Historical Revisionism is taking place then there's really not much more to say. I could, of course, (after returning home) spend hours or days of my time digging up article after article from the 1980's and 1990's in which the history as I state it is there in black and white for you to see but, no, I've been down that road before. After spending (wasting!) all that time you will merely pull something else out of your hat. Believe as you wish. I am sure that some of you here remember well enough but you'd be booted out of the Evolutionists-R-Us Club should you dare say anything.

jorge

Does it even matter? And look at the Kettle calling the Pot black. There is not a more forgetful bunch in terms of seeping under the rug what they got WRONG than the YEC crowd. So what is the 'set of evidences for YEC' du jour Jorge over against those in 2000, or 1990, or 1980?

What you fail to realize Jorge is that science is a continuous process of learning. Learning, refining, getting better, more accurate, this is what its all about.

Your side, OTOH, is all about codifying and dodging the appearance of error. Because you ostensibly think your position is God revealed, and therefore nothing can be wrong, so 'correction' is NOT part of the process.

So to you, pulling back from the idea of junk DNA is some kind of major faux pas that prooooooves you were right, right, right. To anyone with half a brain it just means we are learning more. The aspects of DNA that produced the observation 'junk' are still there. We just understand more about how it all fits together. And not only that, when new data contradicts old conclusions, it gets published and talked about, not buried and ignored as it does in YEC land (e.g. Sarfati STILL tries to claim their aren't any SNR's older than 10,000 years).

What YOU can't deal with is the fact that at least some of the 'junk' DNA is in fact RE-PURPOSED DNA. And as I pointed out in my post which you ignored, we have observational proof that DNA once coded for artifacts known to be a part of the animal's ancestry (Activated genes producing teeth in a bird - a chicken - your mascot) now sits buried in its DNA in a more or less inactive state. This simply DOES NOT FIT any sort of YEC paradigm - BUT IS EXPECTED IN AN EVOLUTIONARY ONE. And you know it. But then again, that is why you 'missed' the post where I pointed this little snag out earlier.



Jim

[Jorge]

We all see how you ducked the issue and tried to change the subject there.

I didn't "duck" anything, you Yo-Yo.

I commented directly to the point of "Wells does not reliably present science in his book."
I also clearly stated - "clearly" except to the comprehension-impaired as yourself - that I have to
wait until I'm home where I will have access to Wells' book and evidence contained therein.

Jorge