What about the DNA evidence?

[Loudmouth]

The consensus isn't nearly as dogmatic as you tend to be over a wide range of topics.

There is nothing dogmatic about it.

Define "selectable function".

Function that affects fitness and is dependent on the sequence of DNA.

You can say it all you like, but that doesn't mean it's *actually true* that 80 percent of all human DNA is "non-functional". You simply don't know what that function might be yet.

I have said time and time again that it is not absolute proof, but it is evidence. Do you need to me to cite those specific posts to show you that my position is not dogmatic?

 

[Michael]

There is nothing dogmatic about it.

There is something dogmatic about they way you're presenting the data (as gospel for all time).

Function that affects fitness and is dependent on the sequence of DNA.

So which DNA strands affect the fight instinct?

I have said time and time again that it is not absolute proof, but it is evidence. Do you need to me to cite those specific posts to show you that my position is not dogmatic?

You'll need to show me some posts where you've addressed the personal identity aspects in those numbers and left room for gaining a further understanding of DNA. So far I haven't seen it.

 

[Loudmouth]

I still have no idea what you personally mean by the term "functional".

What did you mean when you were sure there was function within that 80%?

Your basic position is that "since we cannot figure out what everything does yet, we can just *assume* that what we haven't figure out yet isn't necessary at all". I don't believe that is true.

No, it isn't. My position is that we can use the tools available to us to determine the probability of a DNA sequence having selectable function. That tool is comparative genomics, and it allows us to detect selection for stretches of DNA. DNA under selection has a high probability of having function. DNA that accumulates mutations at the same rate as the mutation rate has a low probability of having function.

Yes, we should go through the genome bit by bit and determine exactly what it does, but that type of survey just isn't within our grasp right now. What is in our grasp are algorithms and population genetics which can tell us the best places to look for function, and which are the poorest. As it turns out, using the tools we have, 80% of the human genome is indistinguishable from DNA where its sequence just doesn't matter. If you have evidence otherwise, I am all ears.

 

[sfs]

I'm simply pointing out that he's making *huge* assumptions and stating them as absolute fact based on a pretty limited understanding of DNA and how it all works. I'm sure there is indeed 'junk' DNA, but simply lack belief that 80 percent of our DNA serves no useful purpose.

As far as I can tell, you're not actually reading any of our responses. The reason for thinking that much human DNA has no function has absolutely nothing to do with our understanding of how it works, or what functions different parts might have.

 

[Loudmouth]

There is something dogmatic about they way you're presenting the data (as gospel for all time).

You are projecting your own emotions onto me.

So which DNA strands affect the fight instinct?

Specifically, we don't know. What we do know are the sections of DNA that are accumulating mutations at a rate that is indistinguishable from DNA that has no function. I have said this over and over. There is nothing dogmatic about it.

You'll need to show me some posts where you've addressed the personal identity aspects in those numbers and left room for gaining a further understanding of DNA. So far I haven't seen it.

 

[Michael]

As far as I can tell, you're not actually reading any of our responses. The reason for thinking that much human DNA has no function has absolutely nothing to do with our understanding of how it works, or what functions different parts might have.

You personally consistently use terms like 'much' that don't push any of my buttons, or make me cringe. On the other hand LM has been running around consistently and dogmatically championing that 80 percent figure like it's gospel. It turns out however (in the other thread on the same topic) that his own references range from 12 percent identified function to *80 percent identified* function, and apparently the only difference between the two references that personally he handed me were the definition of the term *function*. What's up with that dogmatic 80 percent figure?

It's really his dogmatic attitude that bugs me, not the concept that *much* dna might not have a defined function yet.

 

[Loudmouth]

You personally consistently use terms like 'much' that don't push any of my buttons, or make me cringe. On the other hand LM has been running around consistently and dogmatically championing that 80 percent figure like it's gospel. It turns out however (in the other thread on the same topic) that his own references range from 12 percent identified function . . .

And already you fail the reading comprehension test. The abstract I showed you did not say that 12 percent of the genome had identified function:

"We developed an algorithm to measure constraint on the basis of similarity of DNA topography among multiple species, using hydroxyl radical cleavage patterns to interrogate the solvent-accessible surface area of DNA. This algorithm found that 12% of bases in the human genome are evolutionarily constrained-double the number detected by nucleotide sequence-based algorithms."
Local DNA topography correlates with functional nonc... [Science. 2009] - PubMed - NCBI

Do you see any use of the word "function" in that quote? I sure don't.

You are projecting your own emotions on to me.

to *80 percent identified* function, and apparently the only difference between the two references that personally he handed me were the definition of the term *function*. What's up with that dogmatic 80 percent figure?

For the 80 percent function figure, what is the definition of function that they use?

What definition would you like to use?

It's really his dogmatic attitude that bugs me, not the concept that *much* dna might not have a defined function yet.

And yet I have cited scientific, empirical data that supports my conclusions, and I have stated over and over that I am open to any evidence you would like to present. You, on the other hand, reject that most of the genome is without sequence specific function because . . . well, you don't like the idea.

 

[Michael]

And already you fail the reading comprehension test. The abstract I showed you did not say that 12 percent of the genome had identified function:

No, but your first paper claimed it identified the function of *80 percent* of the genome *in addition to* the protein aspects.

"We developed an algorithm to measure constraint on the basis of similarity of DNA topography among multiple species, using hydroxyl radical cleavage patterns to interrogate the solvent-accessible surface area of DNA. This algorithm found that 12% of bases in the human genome are evolutionarily constrained-double the number detected by nucleotide sequence-based algorithms."
Local DNA topography correlates with functional nonc... [Science. 2009] - PubMed - NCBI

Do you see any use of the word "function" in that quote? I sure don't.

Do you see the term "junk DNA" in either paper? I sure don't.

You are projecting your own emotions on to me.

No, I'm just noting that you're winging your claims and you've yet to provide any references that claimed that 80 percent of the genome is 'junk DNA". When can I expect to see that, or see you retract that statement?

For the 80 percent function figure, what is the definition of function that they use?

What definition would you like to use?

I'm fine with your first reference, but apparently you're not. This is where that deja-vu feeling about the neuron debate comes in.

And yet I have cited scientific, empirical data that supports my conclusions,

Not that first paper I looked it. It actually sank your ship just like you neuron reference.

and I have stated over and over that I am open to any evidence you would like to present. You, on the other hand, reject that most of the genome is without sequence specific function because . . . well, you don't like the idea.

I don't like the idea of you running around pulling that 80 percent figure out of your back pocket and never supporting your claims about 'junk dna'.

I'm sure that *some* DNA is in fact unnecessary. I have seen you provide *zero* evidence to support your claim that 80 percent of it is 'junk'.

 

[Loudmouth]

No, but your first paper claimed it identified the function of *80 percent* of the genome *in addition to* the protein aspects.

What was their definition for function?

Do you see the term "junk DNA" in either paper? I sure don't.

No, which means that one of those definitions of functional could include junk DNA, and one of them does. The definition of function used in the ENCODE paper includes junk DNA as being functional.

No, I'm just noting that you're winging your claims and you've yet to provide any references that claimed that 80 percent of the genome is 'junk DNA". When can I expect to see that, or see you retract that statement?[/quote

The 80% was a low estimate based on an amalgam of different papers I have read. I remembered there being something similar in the ENCODE paper, but I am unable to find it so I might have misremembererd. Needless to say, the 80% is on the low end, I have cited papers with values for you to reference, and sfs (an author on many genetics papers) agrees that 80% is within range of the current scientific consensus. What more do you want?

I'm fine with your first reference, but apparently you're not.

What definition for functional do you want to use? Spell it out for us.

This is where that deja-vu feeling about the neuron debate comes in.

Trying to derail yet again.

I'm sure that *some* DNA is in fact unnecessary. I have seen you provide *zero* evidence to support your claim that 80 percent of it is 'junk'.

I have now supplied several peer reviewed papers that state 80% or more of the human genome is not under evolutionary constraint. Why are you ignoring it?

 

[Michael]

What was their definition for function?

Apparently they involve biochemical reactions.

No, which means that one of those definitions of functional could include junk DNA, and one of them does. The definition of function used in the ENCODE paper includes junk DNA as being functional.

It never used the term "junk" at all, nor did your second reference, in fact you're the only person using it!

The 80% was a low estimate based on an amalgam of different papers I have read. I remembered there being something similar in the ENCODE paper, but I am unable to find it so I might have misremembererd.

Apparently you remembered it the wrong way around in the ENCODE paper. They claimed from the start to have isolated the function of 80 percent of the genome, *in addition to* the well understood protein parts.

Needless to say, the 80% is on the low end, I have cited papers with values for you to reference, and sfs (an author on many genetics papers) agrees that 80% is within range of the current scientific consensus. What more do you want?

Scientists discover double meaning in genetic code | UW Today

I want you recognize that we're learning new things about DNA all the time. I want you to realize that with all the variations in human beings, including their various sensitivities to certain foods, their instincts, and parts of their personality are probably all "encoded" in that DNA. You can't just *assume* that it's "junk" just because we don't understand it's function *yet*.

What definition for functional do you want to use? Spell it out for us.

What *exactly* (cite the line please) was wrong with that ENCODE definition of function?

I have now supplied several peer reviewed papers that state 80% or more of the human genome is not under evolutionary constraint. Why are you ignoring it?

The term 'not under evolutionary constraint" does not equal "junk dna". Try again.

 

[Loudmouth]

Apparently they involve biochemical reactions.

Junk DNA is also involved in biochemical reactions. Their definition for functional includes junk DNA.

Apparently you remembered the the wrong way around in the ENCODE paper.

So you are going to ignore the peer reviewed papers and instead focus on lapses in my memory? Can you be more petty?

They claimed from the start to have isolated the function of 80 percent of the genome, *in addition to* the well understood protein parts.

Yes, and their definition of functional is so broad that it includes junk DNA.

I want you recognize that we're learning new things about DNA ll the time.

I want you to recognize what we have learned.

I want you to realize that with all the variations in human beings, including their various sensitivities to certain foods, their instincts, and parts of their personality are probably all "encoded" in that DNA.

You are forgetting that environment also has effects on phenotype independent of genotype. Also, small differences in non-genetic conditions early in development can produce larger changes later on, even in genetically identical individuals. For example, I have brothers who are identical twins. They are clones. Guess what? They have different personalities. They even have different fingerprints.

Brain development is partially guided by genetics, and it is also guided by the environment. You have also yet to show that any brain development is guided by junk DNA.

You can't just *assume* that it's "junk" just because we don't understand it's function *yet*.

I am not assuming it, as has been shown to you several times. More than 80% of the genome is not under evolutionary constraint meaning that it is accumulating mutations at a rate consistent with no function.

What *exactly* (cite the line please) was wrong with that ENCODE definition of function?

Their definition includes junk DNA. That's the major problem. If you gave them 100 million bases of random DNA, they would find function in that random code using their definition.

Do you really think that 60-70% of the human genome is impervious to deleterious mutations? Do you think that you can change every base of 60-70% of our genome and it will still have the same function as it had before?

The term 'not under evolutionary constraint" does not equal "junk dna". Try again.

Yes, it does. That's the whole point. If the sequence can be changed to anything you like and it does not impact fitness, then it is disposable. It is junk.

 

[Loudmouth]

Perhaps this will help people understand why the definition of funcitonal used by the ENCODE people was so poor.

Genome Biol Evol. 2013;5(3):578-90.
On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE.
Graur D, Zheng Y, Price N, Azevedo RB, Zufall RA, Elhaik E.

Abstract


A recent slew of ENCyclopedia Of DNA Elements (ENCODE) Consortium publications, specifically the article signed by all Consortium members, put forward the idea that more than 80% of the human genome is functional. This claim flies in the face of current estimates according to which the fraction of the genome that is evolutionarily conserved through purifying selection is less than 10%. Thus, according to the ENCODE Consortium, a biological function can be maintained indefinitely without selection, which implies that at least 80 - 10 = 70% of the genome is perfectly invulnerable to deleterious mutations, either because no mutation can ever occur in these "functional" regions or because no mutation in these regions can ever be deleterious. This absurd conclusion was reached through various means, chiefly by employing the seldom used "causal role" definition of biological function and then applying it inconsistently to different biochemical properties, by committing a logical fallacy known as "affirming the consequent," by failing to appreciate the crucial difference between "junk DNA" and "garbage DNA," by using analytical methods that yield biased errors and inflate estimates of functionality, by favoring statistical sensitivity over specificity, and by emphasizing statistical significance rather than the magnitude of the effect. Here, we detail the many logical and methodological transgressions involved in assigning functionality to almost every nucleotide in the human genome. The ENCODE results were predicted by one of its authors to necessitate the rewriting of textbooks. We agree, many textbooks dealing with marketing, mass-media hype, and public relations may well have to be rewritten.

On the immortality of television sets: "fun... [Genome Biol Evol. 2013] - PubMed - NCBI
​

In the full article, they go on to say that you have a meaningless definition of function with respect to a tv if millions of years of rust, decay, and damage do nothing to change that function. For example, if you define the function of a tv as being able to have dust stick to it then some piece of that tv may very well keep that function for millions of years, but is that really how we look at functionality in tv's?

 

[Michael]

Junk DNA is also involved in biochemical reactions. Their definition for functional includes junk DNA.

Ya know, I suppose the term "junk dna" has always bugged me and that's part of the issue. The notion that DNA which we do not understand is 'junk' or 'garbage' seems about as silly to me as suggesting that 'missing mass' is necessarily composed of exotic forms of matter, and every unidentified flying object is necessarily from another planet. There's no logical reason for *assuming* it's useless like that.

So you are going to ignore the peer reviewed papers and instead focus on lapses in my memory? Can you be more petty?

So far you haven't given me much to work with. I'll try, but I can't even find the term "junk" in the those first two citations, and the first one I read put the 80 percent figure into the *functional* column, and never used the term "junk" at all.

Yes, and their definition of functional is so broad that it includes junk DNA.

I don't really know that. I know you and probably a *lot* others may feel that way since 80 percent the *other* way now "feels" high to me as well. There's probably some wiggle room on both ends now.

I want you to recognize what we have learned.

What about that recent article? Did you learn anything about the need not to jump to any hasty conclusions?

You are forgetting that environment also has effects on phenotype independent of genotype. Also, small differences in non-genetic conditions early in development can produce larger changes later on, even in genetically identical individuals. For example, I have brothers who are identical twins. They are clones. Guess what? They have different personalities. They even have different fingerprints.

I'm not suggesting that nurture isn't a part of personality, I'm simply saying that nature is also likely to play a role.

Brain development is partially guided by genetics, and it is also guided by the environment. You have also yet to show that any brain development is guided by junk DNA.

Well, brain development is definitely guided by DNA. You also can't demonstrate 80 has *no* effect on human development. That 'doubt' works both ways.

I am not assuming it, as has been shown to you several times. More than 80% of the genome is not under evolutionary constraint meaning that it is accumulating mutations at a rate consistent with no function.

That's just a slogan at this point. The fact it's not under evolutionary constraint does not mean it has no function. You're still jumping to *strong* conclusions based on *weak* evidence at best!

Their definition includes junk DNA.

So you say. I'm going to skip the irrelevant questions

Yes, it does. That's the whole point. If the sequence can be changed to anything you like and it does not impact fitness, then it is disposable. It is junk.

The term "fitness" becomes a 'catch all' for "I don't see any obvious physical deformity as a result of that change". That's not necessarily the only thing that results in the 'fitness' of that creature in terms of it's likelihood of procreating itself. Again, personality aspects (fight vs. flight tendencies) also play a role in that "fitness' aspect.

 

[Michael]

Perhaps this will help people understand why the definition of funcitonal used by the ENCODE people was so poor.

Genome Biol Evol. 2013;5(3):578-90.
On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE.
Graur D, Zheng Y, Price N, Azevedo RB, Zufall RA, Elhaik E.

Abstract


A recent slew of ENCyclopedia Of DNA Elements (ENCODE) Consortium publications, specifically the article signed by all Consortium members, put forward the idea that more than 80% of the human genome is functional. This claim flies in the face of current estimates according to which the fraction of the genome that is evolutionarily conserved through purifying selection is less than 10%. Thus, according to the ENCODE Consortium, a biological function can be maintained indefinitely without selection, which implies that at least 80 - 10 = 70% of the genome is perfectly invulnerable to deleterious mutations, either because no mutation can ever occur in these "functional" regions or because no mutation in these regions can ever be deleterious. This absurd conclusion was reached through various means, chiefly by employing the seldom used "causal role" definition of biological function and then applying it inconsistently to different biochemical properties, by committing a logical fallacy known as "affirming the consequent," by failing to appreciate the crucial difference between "junk DNA" and "garbage DNA," by using analytical methods that yield biased errors and inflate estimates of functionality, by favoring statistical sensitivity over specificity, and by emphasizing statistical significance rather than the magnitude of the effect. Here, we detail the many logical and methodological transgressions involved in assigning functionality to almost every nucleotide in the human genome. The ENCODE results were predicted by one of its authors to necessitate the rewriting of textbooks. We agree, many textbooks dealing with marketing, mass-media hype, and public relations may well have to be rewritten.

On the immortality of television sets: "fun... [Genome Biol Evol. 2013] - PubMed - NCBI
​

In the full article, they go on to say that you have a meaningless definition of function with respect to a tv if millions of years of rust, decay, and damage do nothing to change that function. For example, if you define the function of a tv as being able to have dust stick to it then some piece of that tv may very well keep that function for millions of years, but is that really how we look at functionality in tv's?

Hey! Something useful to work with! I'll tell you what...

I'll take the time to read it before I comment but it may not be until after work today. I'll grant you that the 80 percent figure sounds fishy to me in either direction.

 

[Loudmouth]

Ya know, I suppose the term "junk dna" has always bugged me and that's part of the issue. The notion that DNA which we do not understand is 'junk' or 'garbage' seems about as silly to me as suggesting that 'missing mass' is necessarily composed of exotic forms of matter, and every unidentified flying object is necessarily from another planet. There's no logical reason for *assuming* it's useless like that.

That is not the definition I am using for junk DNA. As sfs said earlier, junk DNA is DNA that is freely accumulating mutations. If DNA has function then some mutations must be deleterious, and we would be able to detect selection against deleterious mutations. It is the positive knowledge that we have about DNA that allows us to differentiate between junk DNA and constrained DNA.

As you have stated, it is nearly impossible to prove a negative. In the case of junk DNA, we are proving a positive, or at least evidencing it, by measuring divergence rates.

So far you haven't given me much to work with. I'll try, but I can't even find the term "junk" in the those first two citations, and the first one I read put the 80 percent figure into the *functional* column, and never used the term "junk" at all.

We can go back to concept of what junk DNA was by the guy who came up with the term.

The points I wish to make are: 1) Natural selection is an extremely conservative force. So long as a particular function is assigned to a single gene locus in the genome, natural selection only permits trivial mutations of that locus to accompany evolution. 2) Only a redundant copy of a gene can escape from natural selection and while being ignored by natural selection can accumulate meaningful mutation to emerge as a new gene locus with a new function. Thus, evolution has been heavily dependent upon the mechanism of gene duplication. 3) The probability of a redundant copy of an old gene emerging as a new gene, however, is quite small. The more likely fate of a base sequence which is not policed by natural selection is to become degenerate. My estimate is that for every new gene locus created about 10 redundant copies must join the ranks of functionless DNA base sequence. 4) As a consequence, the mammalian genome is loaded with functionless DNA.
Susumu Ohno​

This is the concept we are using now for junk DNA. It is DNA that is accumulating mutations because it is not under selective pressure. Sections of this junk DNA will still bind proteins, be methylated, and will probably produce low copy number mRNA's. It is still junk, just as a functionless tv will still gather dust. Mere existence is not function, and yet ENCODE counts mere existence as function.

What about that recent article? Did you learn anything about the need not to jump to any hasty conclusions?

No, nothing really new. It is still sequence specific and selectable function which would be within the 10-20% of the genome not counted as junk.

I'm not suggesting that nurture isn't a part of personality, I'm simply saying that nature is also likely to play a role.

I am not disagreeing that nature plays a role. What I am disagreeing with is that there is evidence for junk DNA playing any significant role.

Well, brain development is definitely guided by DNA.

DNA under evolutionary constraint is DNA.

You also can't demonstrate 80 has *no* effect on human development.

I can demonstrate that 80% of our genome is randomly mutating which is inconsistent with that DNA having function.

The fact it's not under evolutionary constraint does not mean it has no function.

I would be happy to admit that there is some wiggle room both ways. There could be false positives and false negatives when using evolutionary constraint. But how can it be wrong by a multiple of 3 or 4? If you want to claim that evolutionary constraint is not good tool for determining function, then you need to come up with something other than flat denial. You need to explain how a DNA sequence can randomly mutate without losing function due to any of those mutations.

The term "fitness" becomes a 'catch all' for "I don't see any obvious physical deformity as a result of that change".

It is determined by conservation of DNA sequence which is measurable.

Again, personality aspects (fight vs. flight tendencies) also play a role in that "fitness' aspect.

Then if DNA is responsible for those traits that DNA sequence will be conserved since deleterious changes will be selected against.

 

[Loudmouth]

Hey! Something useful to work with!

It's the same things I have been saying all along.

 

[Michael]

It's the same things I have been saying all along.

That alone is enough to make me suspicious.

 

[createdtoworship]

sorry to barge in, but this video is on DNA once you get past the intro's , and no it's not about the creator, or about God persay.

Undistputable Proof of God! our One and Only Creator! YOU MUST SEE THIS!!!! - YouTube

 

[[serious]]

sorry to barge in, but this video is on DNA once you get past the intro's , and no it's not about the creator, or about God persay.

Undistputable Proof of God! our One and Only Creator! YOU MUST SEE THIS!!!! - YouTube

An hour and a half? How about you give a recap?

Is it one of the information based arguments?
Probability based?

EDIT: skipped around a bit and saw him drop the information idea. The trouble is, there is no definition of "information" that is both relevant to evolution AND incapable of being created by known natural mechanisms. Here's my standard hypothetical to illustrate that point:

Say you have a region with a bunch of hemoglobin genes. We'll say 10 of them.
1. a duplication event occurs in which an extra copy is created. We now have 11 identical hemoglobin genes
2. a substitution occurs altering the binding affinity of one copy of that hemoglobin providing altered function
3. a deletion occurs of that modified gene. returning the genome to it's original complement of 10 identical hemoglobins.

Now, if information is tied to genetic code, we must have started and stopped with the same amount of info since we started and stopped with the same code.

If information decreased at any point, it must have increased at another step. Thus, information can increase from known random mechanisms of mutation.

If the amount of information did not change at any step of the process, the definition of information being used is irrelevant to evolution.

 

[sfs]

This paper, which is a review of natural selection in plants, has a nice Fig. 1 showing estimates for several diverse species of the fraction of the genome that is functional, and the fraction of that that's coding.