"The case for junk DNA"

[klaus54]

Once again - unbelievable! - you sink to lower depths, O-Mudd.

Everything you wrote above (and in the post after that) is wrong for more than one reason - or as Pauli would have said, "... it's not even wrong." I shan't be wasting my time explaining why since regardless of anything that I present you're going to go on believing what you wish to believe. I would, however, like to know one thing: that teenage chick that a YEC stole from you, was she 'hot'? I mean, given your level of rage, that 'no-good, pilfering' YEC must have really ticked you off.

Jorge

Well, Jim got a the deep and thoughtful answer from you.

You know, I've never seen a person so cowardly and simultaneously bold and arrogant. I bet you got a plethora of atomic wedgies in high school. Ama right?

K54

P.S. I'm still leaning towards the Designer(tm) being German due to the manner he/she/it is able to Gerry-Rig things and still get em to work fairly well.

[oxmixmudd]

Once again - unbelievable! - you sink to lower depths, O-Mudd.

Everything you wrote above (and in the post after that) is wrong for more than one reason - or as Pauli would have said, "... it's not even wrong." I shan't be wasting my time explaining why since regardless of anything that I present you're going to go on believing what you wish to believe. I would, however, like to know one thing: that teenage chick that a YEC stole from you, was she 'hot'? I mean, given your level of rage, that 'no-good, pilfering' YEC must have really ticked you off.

Jorge

And AGAIN Jorge AVOIDS the evidence staring him in the face.

And AGAIN Jorge tries to make this about emotion and 'rage' - when it has nothing to do with either. What I am curious about is whether when you were on a debate team (as you have claimed to be on several occasions) were you TAUGHT to use ad hominem when you began to loose ground? I mean, you repeat the same garbage each time I bring up the activation of the dormant, historical DNA for TEETH in a CHICKEN rather than actually addressing the clear problem it represents for your position, both on the area of Junk DNA, and the evidence FOR evolution. (I bet Jorge wishes he had some dormant DNA in his arguments he could activate so he could start making some sort of argument that has 'teeth' )

As for your hypothesized 'trauma', THAT is idiotic. When my wife and I married, we were BOTH YEC. Now we BOTH are not. No 'stealing' involved anywhere along the way.

Or will you decide you know my history better than I do as well?


Jim

[klaus54]

Jim,

Chicken teeth -- good example. I wonder if anti-evolutionists ever have offspring with tails?

I wonder what's Jorge's explanation for atavisms?

K54

P.S. That particular Tiger tank has a leaky fuel system.

[rwatts]

Jim,

Chicken teeth -- good example. I wonder if anti-evolutionists ever have offspring with tails?

I wonder what's Jorge's explanation for atavisms?

K54

P.S. That particular Tiger tank has a leaky fuel system.

Just thought I'd pop in to see if Jorge has finally read the paper and offered something sensible.

It seems that he's still in rant mode.

[rwatts]

Once again - unbelievable! - you sink to lower depths, O-Mudd.

Everything you wrote above (and in the post after that) is wrong for more than one reason - or as Pauli would have said, "... it's not even wrong." I shan't be wasting my time explaining why since regardless of anything that I present you're going to go on believing what you wish to believe. I would, however, like to know one thing: that teenage chick that a YEC stole from you, was she 'hot'? I mean, given your level of rage, that 'no-good, pilfering' YEC must have really ticked you off.

Jorge

So Jorge, have you read the science paper yet?

It is online.

If I can reasonably understand it to be able to make an argument to you, then you should have no problem understanding it.

[Jorge]

And AGAIN Jorge AVOIDS the evidence staring him in the face.

And AGAIN Jorge tries to make this about emotion and 'rage' - when it has nothing to do with either. What I am curious about is whether when you were on a debate team (as you have claimed to be on several occasions) were you TAUGHT to use ad hominem when you began to loose ground? I mean, you repeat the same garbage each time I bring up the activation of the dormant, historical DNA for TEETH in a CHICKEN rather than actually addressing the clear problem it represents for your position, both on the area of Junk DNA, and the evidence FOR evolution. (I bet Jorge wishes he had some dormant DNA in his arguments he could activate so he could start making some sort of argument that has 'teeth' )

As for your hypothesized 'trauma', THAT is idiotic. When my wife and I married, we were BOTH YEC. Now we BOTH are not. No 'stealing' involved anywhere along the way.

Or will you decide you know my history better than I do as well?

Jim

Beginning with the end, my "trauma" thing is a joke --- everything has to be s-p-e-l-l-e-d out for you people.

Your thing about "ad hominem" has GOT to be the epitome of 'kettle-black-pot' since you and your minions here at TWeb employ ad hominem against me and others as if it were to be out of style by tomorrow morning. In any event, what I write about you is not ad hominem - it is the result of many years of observations. I know that you don't like it but, hey, don't shoot the messenger.

Lastly, you speak of "avoiding evidence". Did you use a dictionary to spell get the spelling correct? I doubt very much (based on your posts) that you have even an inkling about what "evidence" actually is. Of course, you can invoke your Clintonese to ask, "It depends on what is IS."

Jorge

[Ucchedavāda]

At the risk of re-railing(?) the thread, the following paper may be of interest:
Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

It describes a piece of software (GERP++), which detects evolutionary constraint (implying functional significance) using multiple sequence alignments of multiple mammalian genomes. The program estimates the expected number of substitutions at a given site under the assumption of neutrality, and compares this expectation with the observed rate of change at the site. If a site is under evolutionary constraint, then most mutations are expected to be filtered by (purifying) selection.

Based on such estimates, and by picking out regions showing a deficit of substitutions compared to what would be expected under neutrality, a conservative estimated is made that around 6-8% of human genome is subject to evolutionary constraint, and hence functionally significant. Notably, this model does not require prior knowledge of the functionality of a given DNA sequence. However, since this is based on conservation across a MSA, it seems to me that this model would be less likely to be able to detect rapidly evolving regions in the clade of interest (e.g. HLA genes), even if these are highly biologically significant.

[oxmixmudd]

At the risk of re-railing(?) the thread, the following paper may be of interest:
Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

It describes a piece of software (GERP++), which detects evolutionary constraint (implying functional significance) using multiple sequence alignments of multiple mammalian genomes. The program estimates the expected number of substitutions at a given site under the assumption of neutrality, and compares this expectation with the observed rate of change at the site. If a site is under evolutionary constraint, then most mutations are expected to be filtered by (purifying) selection.

Based on such estimates, and by picking out regions showing a deficit of substitutions compared to what would be expected under neutrality, a conservative estimated is made that around 6-8% of human genome is subject to evolutionary constraint, and hence functionally significant. Notably, this model does not require prior knowledge of the functionality of a given DNA sequence. However, since this is based on conservation across a MSA, it seems to me that this model would be less likely to be able to detect rapidly evolving regions in the clade of interest (e.g. HLA genes), even if these are highly biologically significant.

That is really quite an interesting read. Thanks for putting that up. So bottom line, they start with a hypothesis that coding/functional regions are constrained by selective pressures and thus can't vary outside of what selection allows, whereas non-coding regions can change freely as they are not constrained by selective pressure. Taking that hypothesis, code has been written to blindly attempt to identify functional regions of DNA, and then the results of that blind computation have been compared against known functional regions the determine how likely the result is to be correct. The authors have then further optimized the fundamental estimator in a way that allows for larger constrained regions to be identified, and such that a significant improvement in computational order has been realized (it runs a lot faster).

A good task for the YEC crowd would be to understand why a set of hypothesis that are based on the ToE would yield an algorithm capable of blindly finding with high accuracy coding regions of DNA. It makes perfect sense if evolution is true, (it is in fact ingenious and amazing) and is in fact an idea that would not have even likely had a source apart from it. But why would this be true if Evolution was not part of our history, if the DNA was constructed directly and purposefully, and independent of natural selection.


Jim

[shunyadragon]

That is really quite an interesting read. Thanks for putting that up. So bottom line, they start with a hypothesis that coding/functional regions are constrained by selective pressures and thus can't vary outside of what selection allows, whereas non-coding regions can change freely as they are not constrained by selective pressure. Taking that hypothesis, code has been written to blindly attempt to identify functional regions of DNA, and then the results of that blind computation have been compared against known functional regions the determine how likely the result is to be correct. The authors have then further optimized the fundamental estimator in a way that allows for larger constrained regions to be identified, and such that a significant improvement in computational order has been realized (it runs a lot faster).

A good task for the YEC crowd would be to understand why a set of hypothesis that are based on the ToE would yield an algorithm capable of blindly finding with high accuracy coding regions of DNA. It makes perfect sense if evolution is true, (it is in fact ingenious and amazing) and is in fact an idea that would not have even likely had a source apart from it. But why would this be true if Evolution was not part of our history, if the DNA was constructed directly and purposefully, and independent of natural selection.


Jim

I agree it was an interesting reference. My only disagreement is your use of the terms 'blindly following.' This wording is misleading. The processes are not 'blind.' These processes evolved according to natural law to function as they do.

[Jorge]

At the risk of re-railing(?) the thread, the following paper may be of interest:
Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

It describes a piece of software (GERP++), which detects evolutionary constraint (implying functional significance) using multiple sequence alignments of multiple mammalian genomes. The program estimates the expected number of substitutions at a given site under the assumption of neutrality, and compares this expectation with the observed rate of change at the site. If a site is under evolutionary constraint, then most mutations are expected to be filtered by (purifying) selection.

Based on such estimates, and by picking out regions showing a deficit of substitutions compared to what would be expected under neutrality, a conservative estimated is made that around 6-8% of human genome is subject to evolutionary constraint, and hence functionally significant. Notably, this model does not require prior knowledge of the functionality of a given DNA sequence. However, since this is based on conservation across a MSA, it seems to me that this model would be less likely to be able to detect rapidly evolving regions in the clade of interest (e.g. HLA genes), even if these are highly biologically significant.

First: one has to be very careful when working with models. After all, they yield what we put in. Furthermore, the output of models must often be interpreted.

Second (and more important): From day one I have stated that there are TWO 'evolutions'. One, evolution, is good science based on observable, testable phenomena. The other, Evolution, is ideological - part of a metaphysic/worldview/religion - i.e., it is not science. There are aspects of biology that will (and do) follow the former. It is true, for example, that the allele frequencies in populations will vary over time. It is true that there is a (at least some) correlation between genotype and phenotype. It is true that mutations may alter the manifestation of genotype into phenotype. These and other things are true.

But then the Evolutionary religious fruitcakes carry this into their ideological Fantasy World. Those things that we observe and are able to test are extrapolated into meaning that "all present flora and fauna are the result of the Evolutionary progression over billions of years of a single common ancestor."

Are you following me? There is science and then there is religious ideology and what these less-than-honest dimwits do is conflate the two. They practice bait-and-switch thereby fooling the vast majority of people - even themselves. TO WIT: In a post above O-Mudd -- with his usual style -- demonstrates this. He suggests that the YEC crowd now has something to explain. Well, I just did (above). It's very simple - only took me a few lines. All one has to do is to SEPARATE the one (science) from the other (ideology). Of course, this does not serve their agenda and so don't expect them to admit as much.

By the way, I'm not saying that I (necessarily) accept the results of this paper / model. But it might be true - it might be one of those truly scientific aspects of evolution - I don't know enough at this time. Just don't mix the two 'evolutions' as these people routinely do.

Enough for now.

Jorge

[Catholicity]

Well Jorge, if you think you have actual evidence that's better than anything someone here could provide, instead of insulting people, lets see what you have.

[oxmixmudd]

I agree it was an interesting reference. My only disagreement is your use of the terms 'blindly following.' This wording is misleading. The processes are not 'blind.' These processes evolved according to natural law to function as they do.

Careful - I said 'blindly finding', not 'blindly following'.

My use of blind describes the algorithm discussed in the paper. The algorithm is blind as in 'blindfolded'. The algorithm knows nothing a priori about the DNA sequence before it, what within the DNA is coding or known to be active, it simply identifies regions that have a certain internal characteristics. Characteristics that, if evolution describes the history of the associated organism, should also be associated with the currently 'in use' areas. I am not in any way trying to describe the process of evolution itself.

Jim

[oxmixmudd]

Go read the paper before you prattle on Jorge. The program is not an evolutionary 'model'.

Jim

[Carrikature]

I agree it was an interesting reference. My only disagreement is your use of the terms 'blindly following.' This wording is misleading. The processes are not 'blind.' These processes evolved according to natural law to function as they do.

It's always amusing to see you complain about phrasing/terminology then proceed to demonstrate how you misunderstood what was said. The wording was not misleading.

[oxmixmudd]

First: one has to be very careful when working with models. After all, they yield what we put in. Furthermore, the output of models must often be interpreted.

Second (and more important): From day one I have stated that there are TWO 'evolutions'. One, evolution, is good science based on observable, testable phenomena. The other, Evolution, is ideological - part of a metaphysic/worldview/religion - i.e., it is not science. There are aspects of biology that will (and do) follow the former. It is true, for example, that the allele frequencies in populations will vary over time. It is true that there is a (at least some) correlation between genotype and phenotype. It is true that mutations may alter the manifestation of genotype into phenotype. These and other things are true.

But then the Evolutionary religious fruitcakes carry this into their ideological Fantasy World. Those things that we observe and are able to test are extrapolated into meaning that "all present flora and fauna are the result of the Evolutionary progression over billions of years of a single common ancestor."

Are you following me? There is science and then there is religious ideology and what these less-than-honest dimwits do is conflate the two. They practice bait-and-switch thereby fooling the vast majority of people - even themselves. TO WIT: In a post above O-Mudd -- with his usual style -- demonstrates this. He suggests that the YEC crowd now has something to explain. Well, I just did (above). It's very simple - only took me a few lines. All one has to do is to SEPARATE the one (science) from the other (ideology). Of course, this does not serve their agenda and so don't expect them to admit as much.

By the way, I'm not saying that I (necessarily) accept the results of this paper / model. But it might be true - it might be one of those truly scientific aspects of evolution - I don't know enough at this time. Just don't mix the two 'evolutions' as these people routinely do.

Enough for now.

Jorge

I would add that the above is a very good example of how you insulate yourself from any challenges to your beliefs. You have not read the paper. You do not understand the paper, even on a basic level. And you will not ask yourself the question I asked of the generic YEC:

1) WHY - if the genome is designed - would the active coding regions be locatable by statistiaclly analyzing drift based on the assumption that natural selection constrains most drift?

2) WHY - if these 'non-coding' regions are as functional as you propose they MUST be, are they subject to drift and not the same NS constaints the limit drift in the coding regions

3) Why - if we've only been here 6000 years, has there been enough time to allow drift to be used as a quantifier of coding vs. non-coding regions.

This actually reminds me a great deal of how John Martin deals with the issues associated with his Scientific 'Geocentrism'. e.g., We know and expect parallax to be seen in the stars as observed at opposite seasons of the Year because the Earth's orbit creates a baseline over which the parallax manifests. This is obvious, and a decision to look for parallax shifts in observations of the stars falls out naturally from the theory. From a geocentic POV, there is no reason to expect parallax, AND only a very ad hoc explanation can even hope to account for it (e.g. a 'wobble' in the universe itself).

Likewise in this case. The proposition we were created de novo 6000 years ago has NO expectation THIS particular kind of differentiation with the genome would be expected or useful. Yet is follows naturally as a component of evolutionary theory. Further, the YEC POV must react in an ad hoc fashion (or ignore) these kinds of correlations. And they certainly would be incapable of formulating the hypothesis driving this research - it is not a logical consequence of the overall 'theory'.


Jim