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"The case for junk DNA"

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  • Jorge
    replied
    Originally posted by miked570 View Post
    Surely you are not referring to the ENCODE hype?

    Surely you are aware that they have backed off their original claim, and are now saying that, well, they are not really sure what "function" means.

    But if you mean something else, do tell.


    So, God made our genomes susceptible to mutation such that we are doomed to extinction as a result of Sin; yet he also sacrificed himself as Jesus to atone for that sin; we still experience mutation; God also created a couple of error-correcting mechanisms in the very genomes that He cursed to experience mutation...


    I have to wonder if you folks ever just sit back and think, "Holy crap! How can I actually believe such idiotic, contradictory nonsense!"
    You really - I mean REALLY !!! - ought to remain silent regarding things of which you are clueless about. Of course, I know that, like the bull in the china shop, you will continue -- that's what makes you what you are.

    Jorge

    Leave a comment:


  • klaus54
    replied
    Originally posted by Jorge View Post
    Ad hominem gets you nowhere, O-Mudd.

    ...

    ...
    Very nice Straw Man!

    Jorge
    Project much?

    K54

    Leave a comment:


  • klaus54
    replied
    Originally posted by Jorge View Post
    Is it that you are intellectually unable to follow what I've been presenting - is that it?

    I would have thought that my arguments were plain - straightforward enough but I guess I was wrong.

    Jorge
    What arguments? You mean the ol' "Two Evolutions" canard? Evolution works the same way - generation to generation - by mutations worked on by natural selection of phenotypes. Where's the boundary between the "Two Evolutions"? That's right, you can't come up with one. It's your religion that forces you to make the unfounded assertion of "Two Evolutions".

    Your writing is plain-straightforward enough in the sense your English is impeccable, but what you write is abject ginned-up content-less nonsense.

    The devil is the details -- which of course you cannot provide because your "hypotheses" are just hot-air.

    Bear in mind you cannot even provide a plain-straightforward reading of Ge 1:2-3. Some track record for a "Biblical Creationist".

    Lock 'n load and try again -- with substance this time.

    K54

    Leave a comment:


  • miked570
    replied
    Originally posted by Jorge View Post
    My claim was and continues to be that as we learn more and more about these "junk DNA" regions, we will uncover that, "Oops, I guess they weren't junk after all." I stand by that claim and the papers/articles/reports that come out almost daily are supporting my position while demolishing yours. Get a clue.

    Surely you are not referring to the ENCODE hype?

    Surely you are aware that they have backed off their original claim, and are now saying that, well, they are not really sure what "function" means.

    But if you mean something else, do tell.

    I base that prediction - now and as I did over 20 years ago - on my Biblical Creationist worldview. God's creation was essentially "perfect". The decay that has followed as a result of sin gives us what we now have - a corrupted genome subject to mutations and malfunction.
    So, God made our genomes susceptible to mutation such that we are doomed to extinction as a result of Sin; yet he also sacrificed himself as Jesus to atone for that sin; we still experience mutation; God also created a couple of error-correcting mechanisms in the very genomes that He cursed to experience mutation...


    I have to wonder if you folks ever just sit back and think, "Holy crap! How can I actually believe such idiotic, contradictory nonsense!"

    Leave a comment:


  • miked570
    replied
    Originally posted by Jorge View Post
    Perhaps it's because I do not have a PhD in genetics and cell biology...
    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.
    Interesting.

    Leave a comment:


  • Jorge
    replied
    Originally posted by oxmixmudd View Post
    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:
    Ad hominem gets you nowhere, O-Mudd.

    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?
    ANSWER: There are several possibilities: first, genomes were designed and so it is expected that there will be some numerical-statistical aspects to it whatever causation it is attributed to (such as drift or NS constraint). Second, you may have heard that correlation does not imply causation. Third, some statistical correlation is almost always present (even the points on a circle have a positive linear coefficient). Fourth ... errrr ... Is any of this sinking in?

    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
    ANSWER : If I knew the answer to that, you'd be visiting me in Stockholm just as I'm receiving the Nobel.
    My claim was and continues to be that as we learn more and more about these "junk DNA" regions, we will uncover that, "Oops, I guess they weren't junk after all." I stand by that claim and the papers/articles/reports that come out almost daily are supporting my position while demolishing yours. Get a clue.

    I base that prediction - now and as I did over 20 years ago - on my Biblical Creationist worldview. God's creation was essentially "perfect". The decay that has followed as a result of sin gives us what we now have - a corrupted genome subject to mutations and malfunction. Nonetheless, God did not create with 60% - 98% "junk DNA" in the genome. In addition, what I know about information theory tells me that the vast majority of the genome must be functional - there has to be what I refer to as an 'information infrastructure' if information is to be useful. 'nuff on that.

    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.
    ANSWER : What I've written above would answer that. I'll add that it is you/others, not reality, that (1) invented this "drift measure" and, (2) have interpreted the observations to fit into your model. Kind of like what the Medieval-folk did with astronomical observations, physical-chemical observations, medical observations and in other areas.

    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'.
    Very nice Straw Man!

    Jorge
    Last edited by Jorge; 05-21-2014, 11:53 AM.

    Leave a comment:


  • Jorge
    replied
    Originally posted by Catholicity View Post
    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.
    Is it that you are intellectually unable to follow what I've been presenting - is that it?

    I would have thought that my arguments were plain - straightforward enough but I guess I was wrong.

    Jorge

    Leave a comment:


  • oxmixmudd
    replied
    Originally posted by Jorge View Post
    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

    Leave a comment:


  • Carrikature
    replied
    Originally posted by shunyadragon View Post
    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.

    Leave a comment:


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

    Jim

    Leave a comment:


  • oxmixmudd
    replied
    Originally posted by shunyadragon View Post
    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
    Last edited by oxmixmudd; 05-21-2014, 09:15 AM.

    Leave a comment:


  • Catholicity
    replied
    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.

    Leave a comment:


  • Jorge
    replied
    Originally posted by Ucchedavāda View Post
    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

    Leave a comment:


  • shunyadragon
    replied
    Originally posted by oxmixmudd View Post
    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.

    Leave a comment:


  • oxmixmudd
    replied
    Originally posted by Ucchedavāda View Post
    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

    Leave a comment:

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