nPeace
Veteran Member
Sounds correct.
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Remarkably complete’ 3.8-million-year-old cranium of human ancestor discovered in Ethiopia
- Thread starter We Never Know
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Jose Fly
Fisker of men
It's all the data and observations that lead to the same conclusion. We have studied and monitored various sequences and haven't detected any sign of activity. The very nature of some of the sequence types indicates that they aren't likely to be functional (e.g., repeating segments and broken viral segments). We know that with some segments, if they do become functional they cause serious problems, which obviously means in organisms without those problems the segments aren't functional. We know that some people are born without certain segments and are just fine. We also know that organisms like onions have five times as much non-coding DNA as humans, which is odd since onions aren't 5x more complex than us! And as we've been covering, we've even bred organisms that are lacking certain segments and they turn out just fine.
Like with a jigsaw puzzle, when you put all those pieces of evidence together a clear picture emerges....there are DNA segments that are non-functional.
I'm not sure what you mean there.
Do you think it's likely or unlikely that there's life on the moon?
I was responding to the gist of the paper you linked to, where they state that future research should be done into ultra-conserved segments.
I don't understand who you think manipulated data to fit a preconceived idea.
Actually, copies of genetic sequences are made all the time. There's even a fair bit of variation in the number of copies of genes from one person to another.
And is that accurate?It is important, because I don't understand your line of questioning any other way.
Right now you have assumed that I have a "pre-held position that "junk DNA" doesn't exist"
nPeace
Veteran Member
That's not the issue. Why does it matter what I think?
I didn't read that.
Did I say anything about manipulating data? You sure do make a lot of assumptions. If I interpret something to fit a phenomenon, have I manipulated data? I wasn't aware of that, and don't agree.
Again. I don't know when.
Nope.
Jose Fly
Fisker of men
Well to be fair and bigger picture-wise, it really doesn't matter what anyone here posts or thinks about this subject.
But since you and I are discussing it, and you seem to be interested in it enough to spend a fair bit of time on it, it does tend to pique my interest. But at the very least, I hope our discussion has been helpful.
That's okay. If you never meant to accuse anyone of manipulating data or otherwise being unethical in their scientific work, then I apologize for thinking you did.
It's usually when the egg and sperm that eventually produced you were made.
Okay, thanks for clearing that up.
nPeace
Veteran Member
Helpful?Well to be fair and bigger picture-wise, it really doesn't matter what anyone here posts or thinks about this subject.
But since you and I are discussing it, and you seem to be interested in it enough to spend a fair bit of time on it, it does tend to pique my interest. But at the very least, I hope our discussion has been helpful.
You did give your opinion, which differs to mine, and others, of course.
No problem. I'm used to the assumptions. I just point them out, that's all.
I'm trying not to stretch it anymore, but I didn't see that demonstrated.
No problem.
Jose Fly
Fisker of men
Really? Do you disagree that there are non-functional genetic segments? And what "others" are you referring to?
It's pretty well understood that different copy numbers of genetic segments arise during oogenesis and spermatogenesis. If it'd help, I can provide some papers on that.
nPeace
Veteran Member
Apparently you think you are not giving an opinion. How strange. No conclusive evidence, but it's not an opinion.
Let me put it this way then... You give your belief.
I don't recall this long discussion being based on whether or not there are non-functional genetic segments. If that were the case, I would simply ask the question... Does anyone know how much is non-functional, or what segments are, or are not?
I think there was an answer given to that, but I don't think I got any response from you, on if you agree.
...much of this so-called junk plays important roles in the regulation of gene activity. No one yet knows how extensive that role may be.
I thought I explained that already... Researchers.
I'm not sure what you are trying to say. What does that have to do with segments some consider junk?
I would think that any system that makes a backup copy of every piece of data, would do so with the purpose of using them in the event that the original were corrupted. Moreover, it would remember where each copy was taken, and for what purpose it is used. So when anything goes wrong, the backup would be used, therefore preventing any problems.
Do you know of that happening?
ImmortalFlame
Woke gremlin
They asked you a question regarding whether or not you accept that there are non-functional genetic segments. Why don't you answer that?
And the quote you're giving here doesn't address that question. All it says is that SOME junk DNA does have a function. It does not say ALL.
Jose Fly
Fisker of men
First, I know I'm giving my opinions. So no problem there.
Second, again I notice that you're rather eager to try and cast conclusions drawn from scientific studies as "belief" (earlier you categorized them as "assumption"). Why you do that, I have no idea since earlier you indicated that when it comes to the existence of non-functional DNA, you don't care either way.
Well, you and I started our discussion in this thread after I posted some info to you regarding ENCODE's work (which you had cited), and you saying you didn't agree with my statement: "I just hope you now understand that "does something" doesn't necessarily equate to "functional" when talking about things like "junk DNA". To be clear, there are most certainly segments of the human genome that are "junk", in that they're not at all relevant to the function of the organism."
Here is a summary from someone who works in this particular field (CLICK HERE)...
Junk in Your Genome
Transposable Elements: (44% junk)
DNA transposons:
active (functional): <0.1%
defective (nonfunctional): 3%
retrotransposons:
active (functional): <0.1%
defective transposons
(full-length, nonfunctional): 8%
L1 LINES (fragments, nonfunctional): 16%
other LINES: 4%
SINES (small pseudogene fragments): 13%
co-opted transposons/fragments: <0.1% a
aCo-opted transposons and transposon fragments are those that have secondarily acquired a new function.Viruses (9% junk)
DNA viruses
active (functional): <0.1%
defective DNA viruses: ~1%
RNA viruses
active (functional): <0.1%
defective (nonfunctional): 8%
co-opted RNA viruses: <0.1% b
bCo-opted RNA viruses are defective integrated virus genomes that have secondarily acquired a new function.Pseudogenes (1.2% junk)
(from protein-encoding genes): 1.2% junk
co-opted pseudogenes: <0.1% c
cCo-opted pseudogenes are formerly defective pseudogenes those that have secondarily acquired a new function.Ribosomal RNA genes:
essential 0.22%
junk 0.19%
Other RNA encoding genes
tRNA genes: <0.1% (essential)
known small RNA genes: <0.1% (essential)
putative regulatory RNAs: ~2% (essential) Protein-encoding genes: (9.6% junk)
transcribed region:
essential 1.8%
intron junk (not included above) 9.6% d
dIntrons sequences account for about 30% of the genome. Most of these sequences qualify as junk but they are littered with defective transposable elements that are already included in the calculation of junk DNA.Regulatory sequences:
essential 0.6%
Origins of DNA replication
<0.1% (essential) Scaffold attachment regions (SARS)
<0.1% (essential) Highly Repetitive DNA (1% junk)
α-satellite DNA (centromeres)
essential 2.0%
non-essential 1.0%%
telomeres
essential (less than 1000 kb, insignificant)
Intergenic DNA (not included above)
conserved 2% (essential)
non-conserved 26.3% (unknown but probably junk)
Total Essential/Functional (so far) = 8.7%
Total Junk (so far) = 65%
Unknown (probably mostly junk) = 26.3%
For references and further information click on the "Genomes & Junk DNA" link in the box
LAST UPDATE: May 10, 2011 (fixed totals, and ribosomal RNA calculations)
Transposable Elements: (44% junk)
DNA transposons:
active (functional): <0.1%
defective (nonfunctional): 3%
retrotransposons:
active (functional): <0.1%
defective transposons
(full-length, nonfunctional): 8%
L1 LINES (fragments, nonfunctional): 16%
other LINES: 4%
SINES (small pseudogene fragments): 13%
co-opted transposons/fragments: <0.1% a
aCo-opted transposons and transposon fragments are those that have secondarily acquired a new function.Viruses (9% junk)
DNA viruses
active (functional): <0.1%
defective DNA viruses: ~1%
RNA viruses
active (functional): <0.1%
defective (nonfunctional): 8%
co-opted RNA viruses: <0.1% b
bCo-opted RNA viruses are defective integrated virus genomes that have secondarily acquired a new function.Pseudogenes (1.2% junk)
(from protein-encoding genes): 1.2% junk
co-opted pseudogenes: <0.1% c
cCo-opted pseudogenes are formerly defective pseudogenes those that have secondarily acquired a new function.Ribosomal RNA genes:
essential 0.22%
junk 0.19%
Other RNA encoding genes
tRNA genes: <0.1% (essential)
known small RNA genes: <0.1% (essential)
putative regulatory RNAs: ~2% (essential) Protein-encoding genes: (9.6% junk)
transcribed region:
essential 1.8%
intron junk (not included above) 9.6% d
dIntrons sequences account for about 30% of the genome. Most of these sequences qualify as junk but they are littered with defective transposable elements that are already included in the calculation of junk DNA.Regulatory sequences:
essential 0.6%
Origins of DNA replication
<0.1% (essential) Scaffold attachment regions (SARS)
<0.1% (essential) Highly Repetitive DNA (1% junk)
α-satellite DNA (centromeres)
essential 2.0%
non-essential 1.0%%
telomeres
essential (less than 1000 kb, insignificant)
Intergenic DNA (not included above)
conserved 2% (essential)
non-conserved 26.3% (unknown but probably junk)
Total Essential/Functional (so far) = 8.7%
Total Junk (so far) = 65%
Unknown (probably mostly junk) = 26.3%
For references and further information click on the "Genomes & Junk DNA" link in the box
LAST UPDATE: May 10, 2011 (fixed totals, and ribosomal RNA calculations)
Who specifically?
We were discussing how different people have different numbers of some genes (i.e., copies), and how how that occurs (during sperm and egg production).
Actually in some cases, having extra copies of genes can have negative results, such as increased susceptibility to a disease. Basically gene copies are just like any other mutation....some are good, some are bad, and some are neither.
nPeace
Veteran Member
Fine.
Me. It's written in the journals Fly. Don't you read them? "Scientists believe. Scientists believed. Scientists assumed." Scientists need to interpret, and they need to have opinions.
Why don't you like to hear those terms? Do they sound too religiousy?
Have we not been telling you these things all along? Well. Maybe listening to Creationist might actually be the best thing for you. Hopefully... I really and truly do hope you find that out before the "door to the ark closes".
I don't now understand this. I see you still have not learned from the past. If it's another bad habit, all you have to do is try... try to stop assuming.
Perhaps it runs deeper than you realize. Might it have something to do with ego, do you think?
nPeace
Veteran Member
It makes no sense, imo, going through this again.
I think you came here with a priori assumption, not based on any observation from direct testing, that over 90% of DNA is junk.
Then on the same premise - no direct observation from any testing, you claim, as some scientists assume, that it must be this way because "you don't want most of them to be functional".
That's based on opinion, and not experimental observation.
Other organisms function just fine, with loads of functional DNA.
Then you bring an experiment, which I only just realized in twelve years old, claiming that it supports the view that sections are indeed useless, when in fact the experiment did not prove that.
The evidence was both insufficient and inconclusive.
If something's inconclusive, that means it doesn't lead to a conclusion or a resolution. Inconclusive often describes scientific results. If your data about [X] is inconclusive, then your results don't prove anything.
Aside from the paper you presented, which acknowledges the study was inconclusive, here is one more, much more recent - about seven years later than yours.
Defining functional DNA elements in the human genome
These findings suggest that the noncoding regions of the human genome harbor a rich array of functionally significant elements with diverse gene regulatory and other functions.
...it is important to recognize that there is no universal definition of what constitutes function, nor is there agreement on what sets the boundaries of an element. Both scientists and nonscientists have an intuitive definition of function, but each scientific discipline relies primarily on different lines of evidence indicative of function. Geneticists, evolutionary biologists, and molecular biologists apply distinct approaches, evaluating different and complementary lines of evidence.
The methods also differ widely in their false-positive and false-negative rates, the resolution with which elements are defined, and the throughput with which they can be surveyed. Moreover, each approach remains incomplete, requiring continued method development (both experimental and analytical) and increasingly large datasets (additional species, assays, cell types, variants, and phenotypes). It is thus not surprising that the methods vary considerably with respect to the specific elements they identify. However, the extent of the difference is much larger than simply technical limitations would suggest, challenging current views and definitions of genome function.
However, the scale of the ENCODE Project survey of biochemical activity (across many more cell types and assays) led to a significant increase in genome coverage and thus accentuated the discrepancy between biochemical and evolutionary estimates. This discrepancy led to much debate both in the scientific literature and in online forums, resulting in a renewed need to clarify the challenges of defining function in the human genome and to understand the sources of the discrepancy.
Genetic Approach [has Limitations].
...the evolutionary approach also has limitations.
Finally, although the evolutionary approach has the advantage that it does not require a priori knowledge of what a DNA element does or when it is used, it is unlikely to reveal the molecular mechanisms under selection or the relevant cell types or physiological processes. Thus, comparative genomics requires complementary studies.
The biochemical approach for identifying candidate functional genomic elements complements the other approaches, as it is specific for cell type, condition, and molecular process. ... Although the extent to which individual features contribute to function remains to be determined, they provide a useful surrogate for annotating candidate enhancers and other types of functional elements.
WHAT FRACTION OF THE HUMAN GENOME IS FUNCTIONAL?
Limitations of the genetic, evolutionary, and biochemical approaches conspire to make this seemingly simple question difficult to answer.
...for multiple reasons discussed below, it remains unclear what proportion of these biochemically annotated regions serve specific functions.
...studies have revealed thousands of genetic variants that influence gene expression and regulatory activity. These observations raise the possibility that functional sequences encompass a larger proportion of the human genome than previously thought.
The proportion of the human genome assigned to candidate functions varies markedly among the different approaches, with estimates from biochemical approaches being considerably larger than those of genetic and evolutionary approaches. These differences have stimulated scientific debate regarding the interpretation and relative merits of the various approaches.
Regions with higher signals generally exhibit higher levels of evolutionarily conservation. Thus, one should have high confidence that the subset of the genome with large signals for RNA or chromatin signatures coupled with strong conservation is functional and will be supported by appropriate genetic tests. In contrast, the larger proportion of genome with reproducible but low biochemical signal strength and less evolutionary conservation is challenging to parse between specific functions and biological noise.
It could be argued that some of these regions are unlikely to serve critical functions, especially those with lower-level biochemical signal. However, we also acknowledge substantial limitations in our current detection of constraint, given that some human-specific functions are essential but not conserved and that disease-relevant regions need not be selectively constrained to be functional. Despite these limitations, all three approaches are needed to complete the unfinished process of inferring functional DNA elements, specifying their boundaries, and defining what functions they serve at molecular, cellular, and organismal levels.
Conclusion
Given the limitations of our current understanding of genome function, future work should seek to better define genome elements by integrating all three methods to gain insight into the roles they play in human biology and disease.
...it is important to recognize that there is no universal definition of what constitutes function, nor is there agreement on what sets the boundaries of an element. Both scientists and nonscientists have an intuitive definition of function, but each scientific discipline relies primarily on different lines of evidence indicative of function. Geneticists, evolutionary biologists, and molecular biologists apply distinct approaches, evaluating different and complementary lines of evidence.
The methods also differ widely in their false-positive and false-negative rates, the resolution with which elements are defined, and the throughput with which they can be surveyed. Moreover, each approach remains incomplete, requiring continued method development (both experimental and analytical) and increasingly large datasets (additional species, assays, cell types, variants, and phenotypes). It is thus not surprising that the methods vary considerably with respect to the specific elements they identify. However, the extent of the difference is much larger than simply technical limitations would suggest, challenging current views and definitions of genome function.
However, the scale of the ENCODE Project survey of biochemical activity (across many more cell types and assays) led to a significant increase in genome coverage and thus accentuated the discrepancy between biochemical and evolutionary estimates. This discrepancy led to much debate both in the scientific literature and in online forums, resulting in a renewed need to clarify the challenges of defining function in the human genome and to understand the sources of the discrepancy.
Genetic Approach [has Limitations].
...the evolutionary approach also has limitations.
Finally, although the evolutionary approach has the advantage that it does not require a priori knowledge of what a DNA element does or when it is used, it is unlikely to reveal the molecular mechanisms under selection or the relevant cell types or physiological processes. Thus, comparative genomics requires complementary studies.
The biochemical approach for identifying candidate functional genomic elements complements the other approaches, as it is specific for cell type, condition, and molecular process. ... Although the extent to which individual features contribute to function remains to be determined, they provide a useful surrogate for annotating candidate enhancers and other types of functional elements.
WHAT FRACTION OF THE HUMAN GENOME IS FUNCTIONAL?
Limitations of the genetic, evolutionary, and biochemical approaches conspire to make this seemingly simple question difficult to answer.
...for multiple reasons discussed below, it remains unclear what proportion of these biochemically annotated regions serve specific functions.
...studies have revealed thousands of genetic variants that influence gene expression and regulatory activity. These observations raise the possibility that functional sequences encompass a larger proportion of the human genome than previously thought.
The proportion of the human genome assigned to candidate functions varies markedly among the different approaches, with estimates from biochemical approaches being considerably larger than those of genetic and evolutionary approaches. These differences have stimulated scientific debate regarding the interpretation and relative merits of the various approaches.
Regions with higher signals generally exhibit higher levels of evolutionarily conservation. Thus, one should have high confidence that the subset of the genome with large signals for RNA or chromatin signatures coupled with strong conservation is functional and will be supported by appropriate genetic tests. In contrast, the larger proportion of genome with reproducible but low biochemical signal strength and less evolutionary conservation is challenging to parse between specific functions and biological noise.
It could be argued that some of these regions are unlikely to serve critical functions, especially those with lower-level biochemical signal. However, we also acknowledge substantial limitations in our current detection of constraint, given that some human-specific functions are essential but not conserved and that disease-relevant regions need not be selectively constrained to be functional. Despite these limitations, all three approaches are needed to complete the unfinished process of inferring functional DNA elements, specifying their boundaries, and defining what functions they serve at molecular, cellular, and organismal levels.
Conclusion
Given the limitations of our current understanding of genome function, future work should seek to better define genome elements by integrating all three methods to gain insight into the roles they play in human biology and disease.
Knowing Jose Fly, from experience, of course, I would spend several years still getting the same response from him - no matter how wrong he has been proven to be. I could keep at it, but honestly, I am bored with this subject, since it is going nowhere.
So rather than use up a few more pages clubbing this out, here is what I suggest...
ENCODE is carrying out some specific experiments on these regions of DNA. They are recent, and promise to be meticulous. Perhaps the data you posted is some of those results... I don't know.
When the project is completed in its entirety, you and I can discuss this again. Okay?
In the meantime... just keep in mind that there are many new studies being carried out, all revealing basically the same thing.
19 March 2010
'Junk' DNA gets credit for making us who we are - That stuff is useful after all
Unlike the a priori approach which led to the conclusion that 98% of the genome is useless, these studies are based on experiment and observation.
Jose Fly
Fisker of men
I've not only read them, I have published in them and have participated in the review process.
All I can do is repeat what I said earlier. Science does not operate in such black/white, all-or-none terms where things are either 100% absolutely proven, or they are completely made-up beliefs. And as the work we've been discussing shows, when scientists "assume" they then go out and test those assumptions.
Do you see this as a salvation issue?
What don't you understand? Do you believe all DNA is functional?
Okay, I understand.
No, I personally never gave any type of estimate of how much DNA is non-functional. All I've ever said with that is that there are certain types of DNA that we know are non-functional.
I'm not sure where you got the idea that I "want" any specific outcome. And obviously the conclusion regarding the non-functionality of certain DNA segments is based on experimentation and observation, since that's exactly what we've been citing, quoting, and discussing. The same holds true for the conclusions about certain DNA segments being functional.
I wonder....do you believe that geneticists are up to something? Do you believe they have an ulterior motive when it comes to "junk DNA"?
If you're talking about the mouse knock-out experiment, as the researchers themselves noted, at the very least we can rule out the notion that those segments serve a vital function (otherwise how did the mice survive without them).
Would you like to discuss the contents of that paper?
I'm sorry you've become bored with the subject. I find it extremely interesting. But if you'd prefer to stop talking about it, I understand.
All I can do is reiterate....science does not operate under the sort of black/white, all-or-none framework that you seem to want to impose on it. As I've noted throughout this thread, we've known for a very long time that some non-coding regions are functional, but that doesn't mean that therefore all non-coding regions are functional. We've also known for a while that some specific non-coding regions are non-functional (e.g., short tandem repeats, broken viral sequences, pseudogenes).
In the future, I strongly suggest that you try and minimize black/white thinking when seeking to understand science. And at the very least, I hope this conversation has been helpful.
nPeace
Veteran Member
@Jose Fly when someone says, they don't now understand something, it doesn't mean they don't understand it.
Do you not also understand that when a person says, they think it is pointless to keep repeating a back and forth conversation, that that means they don't want to continue in a "I am right, you are wrong." "No, you are wrong, I am right." conversation.
The conversation will never end. Do you understand that?
Do you not also understand that when a person says, they think it is pointless to keep repeating a back and forth conversation, that that means they don't want to continue in a "I am right, you are wrong." "No, you are wrong, I am right." conversation.
The conversation will never end. Do you understand that?
Jose Fly
Fisker of men
That makes no sense to me......at all. To me, it reads like "When someone says X, they don't mean X".
I understand.
I guess you and I were approaching this discussion from very different angles. I was merely hoping to help you understand some of the subject matter, whereas you saw it as a competition where one of us would emerge victorious and the other defeated.
But I gotta be honest....even that doesn't make sense to me, given how you said the existence of "junk DNA" didn't matter to you one way or the other. Just so you know, that's my view as well. So if that's true, I don't see how there could be a winner and loser, since we both agree.
nPeace
Veteran Member
I understand how you roll Fly.
I did not view it as a competition, but I expect that you can't seem to help yourself from your bad habit of trying to slander other, or paint a bad picture of them to inflate your ego,
So whatever.
Bye.
Jose Fly
Fisker of men
Well earlier you stated that the reason you engaged me was to show that I was wrong.
I did no such thing. I'm not sure why you're reacting this way. I thought we were having a pretty good discussion, and since we are both of the same mind on this subject (we're both okay whether or not "junk DNA" exists), I still don't understand why you're suddenly getting personal like this.
Take care.
nPeace
Veteran Member
Well earlier you stated that the reason you engaged me was to show that I was wrong.
I did no such thing. I'm not sure why you're reacting this way. I thought we were having a pretty good discussion, and since we are both of the same mind on this subject (we're both okay whether or not "junk DNA" exists), I still don't understand why you're suddenly getting personal like this.
Take care.
You said:
I said:
Can you explain how proving someone who adamantly stands on a view you consider wrong, Edit. or proving something wrong, is the same as "a competition where one of us would emerge victorious and the other defeated."?
Do you consider RF to be a competitive forum?
@Jose Fly I edited the post, just in case you miss.
Last edited:
Jose Fly
Fisker of men
Sure. If person A is adamant about a view that person B considers to be wrong, and person B engages person A with the primary intent of debating person A and showing them to be wrong, then the outcome will be something along the lines of "I was right and you were wrong", which is akin to "I won and you lost".
I certainly is at times. Other times it isn't. Every interaction is unique.
Thanks!
nPeace
Veteran Member
What if person B engages person A not with the primary intent of debating person A and showing them to be wrong... Is person B being competitive?