Remarkably complete’ 3.8-million-year-old cranium of human ancestor discovered in Ethiopia

[nPeace]

Then what did you mean when you said "No. I don't understand that"?


I think I'm pretty clear on this topic.

What I meant is, I do not agree with this...
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.

 

[Jose Fly]

What I meant is, I do not agree with this...
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.

Okay then, let's clarify.

Do you disagree that "does something" doesn't necessarily equate to "functional"?

Do you disagree that there are segments of the human genome that serve no function?

 

[nPeace]

Okay then, let's clarify.

Do you disagree that "does something" doesn't necessarily equate to "functional"?

Do you disagree that there are segments of the human genome that serve no function?

What are these... trick questions?
I am not God. It is possible that so called junk DNA is useful.

I think there is a lot we don't know, even though some think they do know.
Since you brought up the question on segments of the gene, I asked a question earlier, which I think was avoided. Do you know which segments of genes are responsible for the function and survival of an organism? As far as I know, no one knows.

A team of scientists at Harvard Medical School may have identified a purpose for at least some junk DNA, according to a study published in Nature. They have discovered a yeast gene, called SRG1, located in a region of DNA long considered a genetic wasteland. Unusually, it does not make a protein, but instead just makes a mRNA (messenger RNA) copy of itself. mRNA usually acts as an intermediary molecule between a gene and the protein it codes for but, in the case of SRG1, the RNA does the work - its job is to stop a neighbouring gene from being switched on. 'This doesn't explain all junk DNA. It gives a potential use for some DNA', said team leader Fred Winston.

Junk' DNA Has Important Role, Researchers Find
DNA sequences from regions of what had been viewed as the "dispensable genome" are actually performing functions that are central for the organism. They have concluded that the genes spur an almost acrobatic rearrangement of the entire genome that is necessary for the organism to grow.

Genes called transposons in the single-celled pond-dwelling organism Oxytricha produce cell proteins known as transposases. During development, the transposons appear to first influence hundreds of thousands of DNA pieces to regroup. Then, when no longer needed, the organism cleverly erases the transposases from its genetic material, paring its genome to a slim 5 percent of its original load.

"The transposons actually perform a central role for the cell,"

The term "junk DNA" has been questioned on the grounds that it provokes a strong a priori assumption of total non-functionality.

Scientists cannot claim that genes have no functionality, simply because they assume that to be the case.
Studies are being done that are revealing that assumptions in this case are often wrong.

Non-coding DNA - Wikipedia
In 2013, a new "record" for the most efficient eukaryotic genome was discovered with Utricularia gibba, a bladderwort plant that has only 3% non-coding DNA and 97% of coding DNA. Parts of the non-coding DNA were being deleted by the plant and this suggested that non-coding DNA may not be as critical for plants, even though non-coding DNA is useful for humans. Other studies on plants have discovered crucial functions in portions of non-coding DNA that were previously thought to be negligible and have added a new layer to the understanding of gene regulation.

It is agreed upon, that researchers do not know what those genes are doing. Do you also agree with that?

 

[Subduction Zone]

What are these... trick questions?
I am not God. It is possible that so called junk DNA is useful.

I think there is a lot we don't know, even though some think they do know.
Since you brought up the question on segments of the gene, I asked a question earlier, which I think was avoided. Do you know which segments of genes are responsible for the function and survival of an organism? As far as I know, no one knows.

A team of scientists at Harvard Medical School may have identified a purpose for at least some junk DNA, according to a study published in Nature. They have discovered a yeast gene, called SRG1, located in a region of DNA long considered a genetic wasteland. Unusually, it does not make a protein, but instead just makes a mRNA (messenger RNA) copy of itself. mRNA usually acts as an intermediary molecule between a gene and the protein it codes for but, in the case of SRG1, the RNA does the work - its job is to stop a neighbouring gene from being switched on. 'This doesn't explain all junk DNA. It gives a potential use for some DNA', said team leader Fred Winston.

Junk' DNA Has Important Role, Researchers Find
DNA sequences from regions of what had been viewed as the "dispensable genome" are actually performing functions that are central for the organism. They have concluded that the genes spur an almost acrobatic rearrangement of the entire genome that is necessary for the organism to grow.

Genes called transposons in the single-celled pond-dwelling organism Oxytricha produce cell proteins known as transposases. During development, the transposons appear to first influence hundreds of thousands of DNA pieces to regroup. Then, when no longer needed, the organism cleverly erases the transposases from its genetic material, paring its genome to a slim 5 percent of its original load.

"The transposons actually perform a central role for the cell,"

The term "junk DNA" has been questioned on the grounds that it provokes a strong a priori assumption of total non-functionality.

Scientists cannot claim that genes have no functionality, simply because they assume that to be the case.
Studies are being done that are revealing that assumptions in this case are often wrong.

Non-coding DNA - Wikipedia
In 2013, a new "record" for the most efficient eukaryotic genome was discovered with Utricularia gibba, a bladderwort plant that has only 3% non-coding DNA and 97% of coding DNA. Parts of the non-coding DNA were being deleted by the plant and this suggested that non-coding DNA may not be as critical for plants, even though non-coding DNA is useful for humans. Other studies on plants have discovered crucial functions in portions of non-coding DNA that were previously thought to be negligible and have added a new layer to the understanding of gene regulation.

It is agreed upon, that researchers do not know what those genes are doing. Do you also agree with that?

Your logical fallacy is Hasty Generalization:

Hasty Generalization

The claim about non-coding DNA is not that all of it is without function. Merely that it is most likely that a large portion of it is without function and some of it definitely is. For example broken genes are almost certainly without function.

Meanwhile, when I asked you about how complex an amoeba was there was a reason for it. That simple little critter has a genome 100 times as long as ours. Are you going to say that an amoeba is one hundred times as complex as a human being?



A while back I asked you a question which you ran way from. Never a good sign by the way.

 

[Jose Fly]

What are these... trick questions?
I am not God. It is possible that so called junk DNA is useful.

I think there is a lot we don't know, even though some think they do know.
Since you brought up the question on segments of the gene, I asked a question earlier, which I think was avoided. Do you know which segments of genes are responsible for the function and survival of an organism? As far as I know, no one knows.

A team of scientists at Harvard Medical School may have identified a purpose for at least some junk DNA, according to a study published in Nature. They have discovered a yeast gene, called SRG1, located in a region of DNA long considered a genetic wasteland. Unusually, it does not make a protein, but instead just makes a mRNA (messenger RNA) copy of itself. mRNA usually acts as an intermediary molecule between a gene and the protein it codes for but, in the case of SRG1, the RNA does the work - its job is to stop a neighbouring gene from being switched on. 'This doesn't explain all junk DNA. It gives a potential use for some DNA', said team leader Fred Winston.

Junk' DNA Has Important Role, Researchers Find
DNA sequences from regions of what had been viewed as the "dispensable genome" are actually performing functions that are central for the organism. They have concluded that the genes spur an almost acrobatic rearrangement of the entire genome that is necessary for the organism to grow.

Genes called transposons in the single-celled pond-dwelling organism Oxytricha produce cell proteins known as transposases. During development, the transposons appear to first influence hundreds of thousands of DNA pieces to regroup. Then, when no longer needed, the organism cleverly erases the transposases from its genetic material, paring its genome to a slim 5 percent of its original load.

"The transposons actually perform a central role for the cell,"

The term "junk DNA" has been questioned on the grounds that it provokes a strong a priori assumption of total non-functionality.

Scientists cannot claim that genes have no functionality, simply because they assume that to be the case.
Studies are being done that are revealing that assumptions in this case are often wrong.

Non-coding DNA - Wikipedia
In 2013, a new "record" for the most efficient eukaryotic genome was discovered with Utricularia gibba, a bladderwort plant that has only 3% non-coding DNA and 97% of coding DNA. Parts of the non-coding DNA were being deleted by the plant and this suggested that non-coding DNA may not be as critical for plants, even though non-coding DNA is useful for humans. Other studies on plants have discovered crucial functions in portions of non-coding DNA that were previously thought to be negligible and have added a new layer to the understanding of gene regulation.

It is agreed upon, that researchers do not know what those genes are doing. Do you also agree with that?

Certainly geneticists have found some level of function for some segments of DNA that were previously thought to be "junk". But that doesn't mean that therefore, all segments that were thought to be "junk" are functional. Like I said before, we know there are segments that code for proteins (or even just parts of proteins) that are broken right back down inside the cell as soon as they are made. So it's pretty safe to conclude that those segments are non-functional. There are also long stretches of our genome that are nothing more than tandem repeats (ATATATATATAT over and over and over). They don't code for anything nor do they regulate anything. We also know there are segments of our genome that some people are born without, yet those folks are just fine. They've also done experiments with mice where they take out sections of their DNA and breed them (so their offspring also lack those deleted sections) and the offspring are normal in every way.

So while we can never say with 100% absolute certainty that a section of DNA is non-functional (because, being a negative conclusion there's always the possibility, no matter how remote, that there's some hidden function), we can say with a very high degree of confidence that some DNA segments are indeed non-functional.

As far as what portions of DNA are "responsible for the function and survival of an organism", it depends on the organism. It wasn't that long ago that scientists synthesized a living cell that had only what they'd determined to be the "essential" genetic sequences. So for that organism, yes we do know what is essential for its function and survival. But for every organism on earth? No.

 

[nPeace]

Certainly geneticists have found some level of function for some segments of DNA that were previously thought to be "junk". But that doesn't mean that therefore, all segments that were thought to be "junk" are functional. Like I said before, we know there are segments that code for proteins (or even just parts of proteins) that are broken right back down inside the cell as soon as they are made. So it's pretty safe to conclude that those segments are non-functional. There are also long stretches of our genome that are nothing more than tandem repeats (ATATATATATAT over and over and over). They don't code for anything nor do they regulate anything. We also know there are segments of our genome that some people are born without, yet those folks are just fine. They've also done experiments with mice where they take out sections of their DNA and breed them (so their offspring also lack those deleted sections) and the offspring are normal in every way.

So while we can never say with 100% absolute certainty that a section of DNA is non-functional (because, being a negative conclusion there's always the possibility, no matter how remote, that there's some hidden function), we can say with a very high degree of confidence that some DNA segments are indeed non-functional.

As far as what portions of DNA are "responsible for the function and survival of an organism", it depends on the organism. It wasn't that long ago that scientists synthesized a living cell that had only what they'd determined to be the "essential" genetic sequences. So for that organism, yes we do know what is essential for its function and survival. But for every organism on earth? No.

So would you agree that you are speculating, assuming, and in some cases guessing?

 

[Jose Fly]

So would you agree that you are speculating, assuming, and in some cases guessing?

You'll have to be more specific about what "cases" you're referring to before I can answer.

 

[Willamena]

Africa gets all the cool skulls.

 

[nPeace]

You'll have to be more specific about what "cases" you're referring to before I can answer.

Everything.

 

[Jose Fly]

Everything.

Then no. As I described, we can conclude with a high degree of certainty, and based on direct evidence, that certain genetic sequences are indeed non-functional. No guesswork or assuming necessary.

 

[nPeace]

Then no. As I described, we can conclude with a high degree of certainty, and based on direct evidence, that certain genetic sequences are indeed non-functional. No guesswork or assuming necessary.

Have you made your conclusionst with 100% certainty? Do you know for sure? Do you know what is going on with all regions considered 'junk'?

 

[Jose Fly]

Have you made your conclusionst with 100% certainty?

Of course not. But we are not limited to only choosing between 100% absolute certainty and complete guesswork. Such a black/white, all-or-none framework is not how science operates.

Do you know what is going on with all regions considered 'junk'?

No. But that doesn't mean we don't know what's going on with some of the regions of "junk". Again, we are not limited to "you either know everything or you know nothing", and as above, science does not operate under that sort of simplistic framework.

 

[Subduction Zone]

Africa gets all the cool skulls.

Homo erectus was first found in Java. Much cooler than Neanderthal Man that was first found in Germany.

 

[nPeace]

Of course not. But we are not limited to only choosing between 100% absolute certainty and complete guesswork. Such a black/white, all-or-none framework is not how science operates.


No. But that doesn't mean we don't know what's going on with some of the regions of "junk". Again, we are not limited to "you either know everything or you know nothing", and as above, science does not operate under that sort of simplistic framework.

So can you please explain to me how you are not assuming, nor speculating, nor guessing?

 

[Subduction Zone]

So can you please explain to me how you are not assuming, nor speculating, nor guessing?

Because ideas are tested in various different ways.

Assuming, guessing, and speculating is the sin of creationists. They refuse to put their ideas in the form of a testable hypothesis.

 

[Polymath257]

Have you made your conclusionst with 100% certainty? Do you know for sure? Do you know what is going on with all regions considered 'junk'?

Is it 'just guessing, speculating, or assuming' if the percentage of confidence is 99.999%?

 

[Jose Fly]

So can you please explain to me how you are not assuming, nor speculating, nor guessing?

It's what I described above, and is described in the material you posted earlier (e.g., the ENCODE project). Geneticists do all sorts of things to test whether certain segments of DNA do anything. The most obvious is they basically "look" and see if the segment does anything. As I noted earlier, they've also bred mice that are lacking segments of DNA and studied their offspring. They've also noticed how some people are born lacking specific DNA segments and are just fine.

Maybe you could clarify what you mean by "assuming, speculating, or guessing"? What do you picture when you imagine scientists doing those things?

 

[Subduction Zone]

It's what I described above, and is described in the material you posted earlier (e.g., the ENCODE project). Geneticists do all sorts of things to test whether certain segments of DNA do anything. The most obvious is they basically "look" and see if the segment does anything. As I noted earlier, they've also bred mice that are lacking segments of DNA and studied their offspring. They've also noticed how some people are born lacking specific DNA segments and are just fine.

Maybe you could clarify what you mean by "assuming, speculating, or guessing"? What do you picture when you imagine scientists doing those things?

@nPeace does not seem to realize that claiming "assuming, speculating, guessing" puts the burden of proof upon him. In fact it may be the main reason that he is at least pretending to ignore me. I kept telling him that if he made such a claim the burden of proof is upon him. He does not seem to be able to support those claims at all.

 

[Jose Fly]

@nPeace does not seem to realize that claiming "assuming, speculating, guessing" puts the burden of proof upon him. In fact it may be the main reason that he is at least pretending to ignore me. I kept telling him that if he made such a claim the burden of proof is upon him. He does not seem to be able to support those claims at all.

Interestingly, there's a whole 'nuther wrinkle in the genetics work he posted about "junk DNA" that I don't think he's aware of. I'm hoping we'll get to that eventually and it'll be interesting to see how that goes.

 

[nPeace]

It's what I described above, and is described in the material you posted earlier (e.g., the ENCODE project). Geneticists do all sorts of things to test whether certain segments of DNA do anything. The most obvious is they basically "look" and see if the segment does anything. As I noted earlier, they've also bred mice that are lacking segments of DNA and studied their offspring. They've also noticed how some people are born lacking specific DNA segments and are just fine.

Maybe you could clarify what you mean by "assuming, speculating, or guessing"? What do you picture when you imagine scientists doing those things?

I don't know what papers you are referring to - it would be good if you post the references. However, if you are referring to studies such as this one, which says this...
However, says team leader Edward Rubin, it could be that these regions serve a purpose too subtle to be detected in the tests done on mice. Another explanation is that the regions are so critical that mice, and humans, have several back-up copies, so deleting just one or two of them has no effect.

My question to you, would be, do you know really?
I suggest you like all other researchers do not know. You assume to know.
These researchers honestly admit they don't know, because of what they are learning about the amazing genome - which functions many times better than any computer program ever written.
Many researchers are realizing that what they once thought, is proving to be wrong.
Some researcher however...

New research, is revealing that the so called junk DNA has a significant role in the cell -

Spoiler: New Research

junk dna 2018
junk dna 2019
'Junk' DNA Has Important Role, Researchers Find
The term "junk DNA" was originally coined to refer to a region of DNA that contained no genetic information. Scientists are beginning to find, however, that 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.

Instead, scientists sometimes refer to these regions as "selfish DNA" if they make no specific contribution to the reproductive success of the host organism. Like a computer virus that copies itself ad nauseum, selfish DNA replicates and passes from parent to offspring for the sole benefit of the DNA itself. The present study suggests that some selfish DNA transposons can instead confer an important role to their hosts, thereby establishing themselves as long-term residents of the genome.

satellite DNA, considered to be "junk DNA", plays a crucial role in holding the genome together
...this genetic "junk" performs the vital function of ensuring that chromosomes bundle correctly inside the cell's nucleus, which is necessary for cell survival. And this function appears to be conserved across many species.

Until fairly recently, scientists believed this so-called "junk" or "selfish" DNA did not serve any real purpose.
"But we were not quite convinced by the idea that this is just genomic junk," said Yukiko Yama****a [an American developmental biologist with a BS and PhD in Biophysics]...

Questions and much debate remain around junk DNA.
Scientists have now linked various non-coding sequences to various biological processes and even human diseases. For instance, researchers believe these sequences are behind the development of the uterus and also of our opposable thumbs. A study published in Annals of Oncology last year showed that a non-coding DNA segment acts like a volume knob for gene expression, ultimately influencing the development of breast and prostate cancer. And a study in Nature Genetics this year found mutations outside of gene-coding regions can cause autism.

Exploring the role of non-coding sequences is now an area of intense research. Increasing evidence suggests these noncoding sequences might help cancer defeat treatment, and experts now see them as promising tools for cancer diagnosis.

Despite the number of functions now ascribed to junk DNA, some researchers still believe most of the genetic code is useless.
Please Read The Case for Junk DNA

Imaging in living cells reveals how 'junk DNA' switches on a gene
New video shows how pieces of DNA once thought to be useless can act as on-off switches for genes. A team led by researchers has captured how this 'junk DNA' finds and activates a target gene in living cells. The video allows researchers to see the enhancers as they find and connect to a gene to kick-start its activity.

These pieces of DNA are part of over 90 percent of the genetic material that are not genes. Researchers now know that this "junk DNA" contains most of the information that can turn on or off genes. But how these segments of DNA, called enhancers, find and activate a target gene in the crowded environment of a cell's nucleus is not well understood.

"This study provides the unique opportunity to observe in real time how two regions of DNA interact with each other," said Michal Levo, a postdoctoral research fellow in the Lewis-Sigler Institute. "We can monitor in time where the enhancer and the gene are physically located and simultaneously measure the gene's activity in an attempt to relate these processes."

The video demonstrates that physical contact between the enhancer and the gene is necessary to activate transcription, the first step in reading the genetic instructions. The enhancers stay connected to the gene the entire time it is active. When the enhancer disconnects, gene activity stops.

The researchers also found that during transcription, the structure formed by the enhancer and gene becomes more compact, suggesting a change in the DNA in that region.

Do you know what assume, speculate, and guess mean? If you do, then you can apply that to the claim that you know that all segments that are thought to be, or that you think to be "junk" are non-functional, and don't play any important role to the cell, or organism.