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

[Jose Fly]

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.

All I can do is repeat what I said before....science does not operate under the sort of black/white, all-or-none framework, where you either absolutely 100% know something or you just assume things with no evidence at all.

Specific to the work with mice Rubin's talking about, it's what I described....the scientists conducted a series of experiments, collected the resulting data, analyzed those results, and drew their conclusions.

To me, that's quite different than merely assuming one's conclusions or just empty speculation. What I wonder is, do you recognize the difference between drawing conclusions from experimental data, versus merely assuming the conclusions?

Rubin is also correct to note that there's always the possibility that the deleted sequences have some obscure, undetected function. That's just how science works....nothing is absolute.

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.

Again, all I can do is repeat what I've been saying....science does not operate under the sort of black/white, all-or-none framework, where you either absolutely 100% know something or you just assume things with no evidence at all.

Many researchers are realizing that what they once thought, is proving to be wrong.

Of course. That's why we have science! If we knew everything to 100% certainty, science would be finished, wouldn't it?

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.

We covered this already. Certainly geneticists have found that some sequences that were previously thought to be non-functional, do indeed have a function. But that does not mean all such sequences are therefore functional.

Do you understand that crucial point?

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.

I do know what they mean.

But I asked you what those terms mean to you. So if you could answer this question, I would appreciate it.

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

 

[nPeace]

All I can do is repeat what I said before....science does not operate under the sort of black/white, all-or-none framework, where you either absolutely 100% know something or you just assume things with no evidence at all.

Specific to the work with mice Rubin's talking about, it's what I described....the scientists conducted a series of experiments, collected the resulting data, analyzed those results, and drew their conclusions.

To me, that's quite different than merely assuming one's conclusions or just empty speculation. What I wonder is, do you recognize the difference between drawing conclusions from experimental data, versus merely assuming the conclusions?

Rubin is also correct to note that there's always the possibility that the deleted sequences have some obscure, undetected function. That's just how science works....nothing is absolute.


Again, all I can do is repeat what I've been saying....science does not operate under the sort of black/white, all-or-none framework, where you either absolutely 100% know something or you just assume things with no evidence at all.


Of course. That's why we have science! If we knew everything to 100% certainty, science would be finished, wouldn't it?


We covered this already. Certainly geneticists have found that some sequences that were previously thought to be non-functional, do indeed have a function. But that does not mean all such sequences are therefore functional.

Do you understand that crucial point?


I do know what they mean.

But I asked you what those terms mean to you. So if you could answer this question, I would appreciate it.

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

Guess - estimate or suppose (something) without sufficient information to be sure of being correct.
Speculate - form a theory or conjecture about a subject without firm evidence.
Assume - suppose to be the case, without proof.

Did you address my question, on if you know what these segments of genes do (non-coding regions)?
Would you please address this also...
Can you apply the above definitions 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. How are you not assuming?
If you feel you have answered before, please provide the paper(s) to support your claims.

You said earlier "We also know there are segments of our genome that some people are born without, yet those folks are just fine."
Is that not an assumption that those "missing" genes are not there because you are comparing them with individuals who have more copies and duplication?

 

[Jose Fly]

Guess - estimate or suppose (something) without sufficient information to be sure of being correct.
Speculate - form a theory or conjecture about a subject without firm evidence.
Assume - suppose to be the case, without proof.

Thanks for posting that. So do you believe there isn't "sufficient evidence" or "firm evidence" that certain segments of DNA are non-functional, and that scientists like Rubin are merely "supposing" that they don't have a function?

Did you address my question, on if you know what these segments of genes do (non-coding regions)?

You'll have to be more specific before I can say. Which specific non-coding regions are you asking about?

Would you please address this also...
Can you apply the above definitions 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. How are you not assuming?

Because as the work you cited describes, there is all sorts of evidence that they are non-functional. Geneticists have observed that they don't show any activity, they've bred mice without the segments and tested them in many different ways and found them to be completely normal, and they've found that some people are born lacking certain segments and are completely normal. Finally, with some of the segments their very makeup (simple repeats of ATATATATATAT) indicates that they serve no function.

That's quite a bit of evidence all pointing to the same conclusion....the segments are non-functional.

Is there any evidence at all that they actually do have a function?

You said earlier "We also know there are segments of our genome that some people are born without, yet those folks are just fine."
Is that not an assumption that those "missing" genes are not there because you are comparing them with individuals who have more copies and duplication?

I'm not talking about people with different amounts of genes, I'm talking about people with different amounts of "junk", for example the repeating segments I mentioned earlier (ATATATAT).

 

[nPeace]

Thanks for posting that. So do you believe there isn't "sufficient evidence" or "firm evidence" that certain segments of DNA are non-functional, and that scientists like Rubin are merely "supposing" that they don't have a function?

I have posted many studies that demonstrate 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.
Although they are not important for making protein, they perform other important functions.

It's not about what I believe. I am not the researchers.
I am referring to information that is part of scientific research. If you have a problem with that research, feel free to demonstrate otherwise.

By the way, Ruben acknowledged that "it could be that these regions serve a purpose too subtle to be detected in the tests done on mice".
That is not something to brush aside, because it says that 1) there is not sufficient information to be sure of being correct - a guess. 2) it is not firm evidence, but an opinion or conclusion was formed on the basis of incomplete information - speculation. 3) It is supposed to be the case, without proof - assumption.

Another explanation was also suggested - 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.

Do you disagree that the non-coding regions work with the coding regions, and that you are assuming that they don't, based on "a priori assumption of total non-functionality"?

You'll have to be more specific before I can say. Which specific non-coding regions are you asking about?

Specifically all that you refer to as junk.

Because as the work you cited describes, there is all sorts of evidence that they are non-functional.

Can you please point to what work you are referring to.

Geneticists have observed that they don't show any activity, they've bred mice without the segments and tested them in many different ways and found them to be completely normal, and they've found that some people are born lacking certain segments and are completely normal. Finally, with some of the segments their very makeup (simple repeats of ATATATATATAT) indicates that they serve no function.

That's quite a bit of evidence all pointing to the same conclusion....the segments are non-functional.

You have not provided any paper(s). Is there a reason you didn't, although I asked? Does any exist?

Is there any evidence at all that they actually do have a function?

Yes. I posted a number of them. Did you not look at them? Which do you think is not accurate?

I'm not talking about people with different amounts of genes, I'm talking about people with different amounts of "junk", for example the repeating segments I mentioned earlier (ATATATAT).

What you assume to be junk. Is it not an assumption?

 

[Jose Fly]

I have posted many studies that demonstrate 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.
Although they are not important for making protein, they perform other important functions.

Right, and I believe we covered this before. There's no doubt that geneticists have discovered functions for some of what was previously thought to be "junk", but they certainly have not found functions for all (or even most) "junk".

It's not about what I believe. I am not the researchers.

That's interesting. Let's take a look at some of the info from geneticists you've posted so far.

Let's start with THIS ARTICLE from 2004 about the "knockout mice" (mice that have been bred so that large sections of the genomes are missing), where you've quoted Edward Rubin as saying "it could be that these regions serve a purpose too subtle to be detected in the tests done on mice" and the statement about the SRG1 gene in yeast. You can CLICK HERE to see the actual published paper where their work is fully described.

Interestingly, the abstract concludes with this statement: "These results, while not inclusive of all the possible phenotypic impact of the deleted sequences, indicate that extreme sequence constraint does not necessarily reflect crucial functions required for viability." IOW, at the very least these experiments demonstrate that the sequences that were deleted from the mice are not required for an organism to live, grow, and breed normally. So even if they do have a function, it's one the organism can do just fine without.

But there's something else you should notice in that paper (something I told @Subduction Zone was a "whole 'nuther wrinkle"). It's right there in the very first sentence in the introduction: "Evolutionary conservation has become a powerful means for identifying functionally important genomic sequences. Ultraconserved elements have been defined as a group of extremely conserved sequences that show 100% identity over 200 bp or greater between the human, mouse, and rat genomes". Do you appreciate what that means? They're basically saying that all this work is based on an evolutionary framework, where mice, rats, and humans share a common evolutionary ancestry. That understanding is what tells the geneticists where in those genomes to look and what to look for. Without that understanding, none of this work could have been done in the first place!

Do you appreciate the irony here? You...someone who adamantly denies evolutionary common descent...is citing work that is entirely based on that very concept!

Also, if you're right and evolutionary common descent isn't real, then how do you explain the fact that it generates successful research? If it's completely false, shouldn't the work be a garbled mess?

I am referring to information that is part of scientific research. If you have a problem with that research, feel free to demonstrate otherwise.

I have absolutely no problem at all with the research. It's very well done and their conclusions are very well supported. What do you think of the research?

By the way, Ruben acknowledged that "it could be that these regions serve a purpose too subtle to be detected in the tests done on mice".
That is not something to brush aside, because it says that 1) there is not sufficient information to be sure of being correct - a guess. 2) it is not firm evidence, but an opinion or conclusion was formed on the basis of incomplete information - speculation. 3) It is supposed to be the case, without proof - assumption.

We've covered this already. And as noted in the Rubin et al. paper, even if those segments have a function, it's not at all vital to the survival, development, growth, or reproduction of the organism.

Another explanation was also suggested - 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.

Yep, which would mean the extra copies are just that....extra.

Do you disagree that the non-coding regions work with the coding regions, and that you are assuming that they don't, based on "a priori assumption of total non-functionality"?

In some cases yes (non-coding regions work with coding regions) and in other cases no.

Bigger picture-wise, from what I can tell the primary issue here is you keep trying to force this subject and associated research into a black/white, all-or-none framework. Specifically, you seem to be thinking that if some non-coding regions have a function, then all non-coding segments must be functional.

All I can do is urge you to try to not think in such stark terms when learning about scientific research.

And to be clear, most certainly some non-coding regions are functional. But it's also just as clear that other non-coding regions are non-functional.

Specifically all that you refer to as junk.

That's exactly what I'm talking about above. You can't lump all non-coding DNA into a single category, and draw conclusions about all of it as a whole. There are many, many different types of non-coding DNA, and they all need to be considered individually.

Does that make sense, or should we start going over some of the different types of non-coding DNA?

Can you please point to what work you are referring to.

I was referring to the ENCODE Project that you cited, and how even under their quite generous criteria for something to be "functional", a full 20% of the human genome was determined to not be functional. Does that seem significant to you?

You have not provided any paper(s). Is there a reason you didn't, although I asked? Does any exist?

To be honest, molecular genetics papers are extremely jargon-heavy and difficult for laypeople to understand. For example, one of the categories of "junk DNA" are "long terminal repeats", which are basically genetic viruses that replicate themselves in the genome of their host (e.g., humans). CLICK HERE for the wiki article.

I thought about going over this with you and linking to some papers that support my overall point about certain DNA segments being non-functional (and with LTRs, you don't want most of them to be functional), but given the dense, highly-technical nature of the material, I didn't see a lot of benefit.

To put it bluntly, if you really want to get into a meaningful discussion of "junk DNA", you're going to have to do quite a bit of work to get up to speed on molecular genetics.

Yes. I posted a number of them. Did you not look at them? Which do you think is not accurate?

I was specifically asking about repeating segments (ATATATATAT) and whether you had looked to see if they were functional. Hint: they aren't, and are another category of segments that you don't want to become functional in your genome.

What you assume to be junk. Is it not an assumption?

Again, I urge you to not apply a black/white framework to this research. To most folks, if you told them that geneticists just "assumed" that there was junk-DNA, their impression would be of geneticists not doing any tests, experiments, or other work, and instead just sitting in an office, imagining it to be junk, and writing "it's junk" with no supporting evidence whatsoever.

But as the work you've cited shows, that's not the case at all. Researchers from across the globe have conducted lots and lots of experiments and tests of all kinds to see if they can find functions for many different types of non-coding segments. In some cases they found functions, and with others no matter what they did they could not find any function at all. They even bred mice that were completely lacking in specific segments, and lo and behold....the mice were perfectly normal!

So I hope you understand my point. There is a lot of space between "they just assumed" and "it's been proven". Specific to our subject, there is a lot of evidence that certain types of non-coding DNA are indeed non-functional. So there's no reason to assert that the researchers are merely "assuming" their conclusions. A more accurate description would be, "Based on numerous experiments, studies, and observations, geneticists have concluded that some non-coding DNA serves no function".

Hopefully, you will strive to be accurate when speaking about this material.

 

[nPeace]

Right, and I believe we covered this before. There's no doubt that geneticists have discovered functions for some of what was previously thought to be "junk", but they certainly have not found functions for all (or even most) "junk".

Of course. If they found for all, you would not be able to argue, would you?
That does not mean that all of it is non-functional. An organism survives with multiple copying error, that throw things out of wack, and repaired genes are not perfect, but we live, grow, and reproduce.
However, they do say, "No one yet knows how extensive that role may be."

That's interesting. Let's take a look at some of the info from geneticists you've posted so far.

Let's start with THIS ARTICLE from 2004 about the "knockout mice" (mice that have been bred so that large sections of the genomes are missing), where you've quoted Edward Rubin as saying "it could be that these regions serve a purpose too subtle to be detected in the tests done on mice" and the statement about the SRG1 gene in yeast. You can CLICK HERE to see the actual published paper where their work is fully described.

Thank you for the paper.
Like I said before, do your research, but to claim you have the "bull by the horns", when you are "grabbing the tail", is a mistake made by some people.
These results, while not inclusive of all the possible phenotypic impact of the deleted sequences, indicate that extreme sequence constraint does not necessarily reflect crucial functions required for viability.
What does this say to you.... that they have sufficient information, so as to be sure?
I suggest they are in a dark unfamiliar warehouse, and the lights are not going to come on anytime soon... but they will. I'll wait for the tripping and falling. That's science.
...the full extent of transcription remains an open question that will not be fully addressed until we decipher the complete range and biological diversity of the transcribed genomic sequences.

Interestingly, the abstract concludes with this statement: "These results, while not inclusive of all the possible phenotypic impact of the deleted sequences, indicate that extreme sequence constraint does not necessarily reflect crucial functions required for viability." IOW, at the very least these experiments demonstrate that the sequences that were deleted from the mice are not required for an organism to live, grow, and breed normally. So even if they do have a function, it's one the organism can do just fine without.

But there's something else you should notice in that paper (something I told @Subduction Zone was a "whole 'nuther wrinkle"). It's right there in the very first sentence in the introduction: "Evolutionary conservation has become a powerful means for identifying functionally important genomic sequences. Ultraconserved elements have been defined as a group of extremely conserved sequences that show 100% identity over 200 bp or greater between the human, mouse, and rat genomes". Do you appreciate what that means? They're basically saying that all this work is based on an evolutionary framework, where mice, rats, and humans share a common evolutionary ancestry. That understanding is what tells the geneticists where in those genomes to look and what to look for. Without that understanding, none of this work could have been done in the first place!

Do you appreciate the irony here? You...someone who adamantly denies evolutionary common descent...is citing work that is entirely based on that very concept!

Also, if you're right and evolutionary common descent isn't real, then how do you explain the fact that it generates successful research? If it's completely false, shouldn't the work be a garbled mess?

I don't see any irony.
When one focuses only on things one has some knowledge of, or familiarity with, it's not difficult to find what one are looking for. That's why a mechanic who never saw a V8 engine can find what he is looking for. Or a computer technician can work on capacitors and other technical parts - although different to ones he worked on previously.
Start with a presumption, and fit all the evidence to it. It should work, so long as you are allowed flexibility.
Less than 10% of human DNA has functional role, claim scientists
"Many [DNA] elements that play important roles in human disease are not evolutionarily conserved. Some of these have human-specific functions, some are involved in late-onset diseases like Alzheimer's, and others are simply missed by current comparative genomics methods," said Manolis Kellis, a computational biologist at MIT who was not involved in the study. "We cannot simply ignore the remaining 90% of the genome that is not evolutionarily conserved."

I have absolutely no problem at all with the research. It's very well done and their conclusions are very well supported. What do you think of the research?

So you have no problem with those who disagree with you. That's fine. It's expected that scientists will disagree, and have different opinions. After all, you can't prove something to be true, when you are working within limits, and new studies are sure to turn up new findings.
Recent evidence has suggested that more than 90% of the human genome is transcribed into RNA. However, this view has been strongly contested by groups of scientists who argued that many of the observed transcripts are simply the result of transcriptional noise.
I say, to the scientists, do your best at your job.
Do you agree?

We've covered this already. And as noted in the Rubin et al. paper, even if those segments have a function, it's not at all vital to the survival, development, growth, or reproduction of the organism.

We don't know if that is the complete picture. It's a start.

Yep, which would mean the extra copies are just that....extra.

Why do they have to be extra copies?
When you delete anything on your computer, do you think an extra copy exists?
There are no extra copies, the deleted portion is moved to (inserted in) another area, and stored there.
So if the deleted portion is copied, and inserted somewhere else, the deleted portion is gone, but the copy is now being used.
In that case, the program is working as before, but you don't see anything looking like what you deleted, because it now resides in a section hidden from your eyes.
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 fact that scientists are now learning 1) the significant role of transposons - how they 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. 2) non-coding DNA segment are essential to the fine-tuning of gene expression. 3) "junk DNA" contains most of the information that can turn on or off genes. 4) Segments of "junk DNA" are responsible for performing the first step in reading the genetic instructions.

 

[nPeace]

In some cases yes (non-coding regions work with coding regions) and in other cases no.

How do you know this?

Bigger picture-wise, from what I can tell the primary issue here is you keep trying to force this subject and associated research into a black/white, all-or-none framework. Specifically, you seem to be thinking that if some non-coding regions have a function, then all non-coding segments must be functional.

All I can do is urge you to try to not think in such stark terms when learning about scientific research.

And to be clear, most certainly some non-coding regions are functional. But it's also just as clear that other non-coding regions are non-functional.

Again, you don't know this, do you? If you think you do, just tell me how you know. The paper you refer to does not say so. However, I accept that you want to, and have assumed so, based of course on the a priori assumption, first proposed.

That's exactly what I'm talking about above. You can't lump all non-coding DNA into a single category, and draw conclusions about all of it as a whole. There are many, many different types of non-coding DNA, and they all need to be considered individually.

Does that make sense, or should we start going over some of the different types of non-coding DNA?

It seems to make sense to you to label all non-coding regions as junk. So all I did was the reverse.

I was referring to the ENCODE Project that you cited, and how even under their quite generous criteria for something to be "functional", a full 20% of the human genome was determined to not be functional. Does that seem significant to you?

I said a million times that that was not the only study I referred to. However, you seem to ignore that. Maybe you paid no attention to the other studies I pointed out.

To be honest, molecular genetics papers are extremely jargon-heavy and difficult for laypeople to understand. For example, one of the categories of "junk DNA" are "long terminal repeats", which are basically genetic viruses that replicate themselves in the genome of their host (e.g., humans). CLICK HERE for the wiki article.

I thought about going over this with you and linking to some papers that support my overall point about certain DNA segments being non-functional (and with LTRs, you don't want most of them to be functional), but given the dense, highly-technical nature of the material, I didn't see a lot of benefit.

To put it bluntly, if you really want to get into a meaningful discussion of "junk DNA", you're going to have to do quite a bit of work to get up to speed on molecular genetics.

If I ask for a paper, I think it would be fair to give me, rather than assume I can't read it.
Are you saying this discussion is not meaningful? I could say the same thing, but for the reason that you insist on your opinion.
Every argument I have presented was based on papers from scientists - not me. So that may be why you have addressed none, but the one you thought was easy to argue against - the ENCODE project.

I was specifically asking about repeating segments (ATATATATAT) and whether you had looked to see if they were functional. Hint: they aren't, and are another category of segments that you don't want to become functional in your genome.

Again, I urge you to not apply a black/white framework to this research. To most folks, if you told them that geneticists just "assumed" that there was junk-DNA, their impression would be of geneticists not doing any tests, experiments, or other work, and instead just sitting in an office, imagining it to be junk, and writing "it's junk" with no supporting evidence whatsoever.

The Wikipedia article,as well as hundreds of others said they assumed.
Many say they are wrong to assume.

But as the work you've cited shows, that's not the case at all. Researchers from across the globe have conducted lots and lots of experiments and tests of all kinds to see if they can find functions for many different types of non-coding segments. In some cases they found functions, and with others no matter what they did they could not find any function at all. They even bred mice that were completely lacking in specific segments, and lo and behold....the mice were perfectly normal!

So I hope you understand my point. There is a lot of space between "they just assumed" and "it's been proven". Specific to our subject, there is a lot of evidence that certain types of non-coding DNA are indeed non-functional. So there's no reason to assert that the researchers are merely "assuming" their conclusions. A more accurate description would be, "Based on numerous experiments, studies, and observations, geneticists have concluded that some non-coding DNA serves no function".

Tell me honestly, if a few months or years from now, you read a paper that said, "Scientists had assumed.... but new research shows..." What would you say to me, if I said to you, So they did not assume, right?

Hopefully, you will strive to be accurate when speaking about this material.

Are you saying I am not striving to be accurate, just because I don't accept your opinion, or side with you?
I suggest you get over it. It just requires one to not assume that they are the sole experts on anything to do with science, and recognize that there are other scientists who do research and argue against you, and the scientists you want to agree with.
Despite the number of functions now ascribed to junk DNA, some researchers still believe most of the genetic code is useless.

 

[Jose Fly]

How do you know this?

By looking at all the different information we've been discussing (and more). I've described it multiple times now.

Again, you don't know this, do you? If you think you do, just tell me how you know.

I have explained many different times.

Geneticists have observed that they don't show any activity, they've bred mice without the segments and tested them in many different ways and found them to be completely normal, and they've found that some people are born lacking certain segments and are completely normal. Finally, with some of the segments their very makeup (simple repeats of ATATATATATAT) indicates that they serve no function.

That's quite a bit of evidence all pointing to the same conclusion....the segments are non-functional.

The paper you refer to does not say so. However, I accept that you want to, and have assumed so, based of course on the a priori assumption, first proposed.

It seems you are adamant on imposing your black/white mode of thinking (where something is either 100% absolutely proven, or it is merely assumed) onto scientific research. I've attempted to get you to think beyond that, but you don't seem interested.

Let me ask you this....would you agree that there is evidence that some non-coding regions of DNA are non-functional?

It seems to make sense to you to label all non-coding regions as junk. So all I did was the reverse.

Nope, I never said anything like that at all, and in fact have stated to you before that without a doubt some non-coding regions are functional. So if you could try and remember that, I would appreciate it.

I said a million times that that was not the only study I referred to. However, you seem to ignore that. Maybe you paid no attention to the other studies I pointed out.

I'm not sure why you would say that, since I've also referred to, provided a link to, and quoted from the Rubin et al. work you cited. So again, if you could try and remember that going forward, I would appreciate it.

If I ask for a paper, I think it would be fair to give me, rather than assume I can't read it.
Are you saying this discussion is not meaningful? I could say the same thing, but for the reason that you insist on your opinion.
Every argument I have presented was based on papers from scientists - not me. So that may be why you have addressed none, but the one you thought was easy to argue against - the ENCODE project.

Again, I'm not sure why you think I've not addressed any of the material you've posted (outside of ENCODE), when it's simply a matter of written record that I have (and even did so in the very post you're responding to).

The Wikipedia article,as well as hundreds of others said they assumed.
Many say they are wrong to assume.

Sure, in the very early days of genetics, some geneticists did assume that if a sequence doesn't code for a protein, it must not be functional. But there were other geneticists who thought otherwise. Then over the ensuing years, geneticists have done the work to find out what really is going on. See, that's how science works. As the existence of non-coding regions came to light, some said "it's junk", others said "it's not junk", and then everyone went to work to resolve the question. And as we've seen, it turns out both were sorta right....some regions have a function, others don't.

Tell me honestly, if a few months or years from now, you read a paper that said, "Scientists had assumed.... but new research shows..." What would you say to me, if I said to you, So they did not assume, right?

I'll let you know when something like that happens and more specific details are presented.

Are you saying I am not striving to be accurate, just because I don't accept your opinion, or side with you?

It seems to me you're quite eager to label the existence of non-functional DNA as "assumption" and use that as an excuse to wave away inconvenient information. Perhaps I'm wrong on that, but I do have to wonder why this subject is of such interest to you. Any particular reason?

I suggest you get over it. It just requires one to not assume that they are the sole experts on anything to do with science, and recognize that there are other scientists who do research and argue against you, and the scientists you want to agree with.
Despite the number of functions now ascribed to junk DNA, some researchers still believe most of the genetic code is useless.

I'm not sure what scientists you think are arguing against me, so if you could explain, that'd be helpful.

Finally, I noticed you entirely ignored the fact that the work you've been citing is based on the understanding of evolutionary common ancestry between rats, mice, and humans. Care to explain why?

 

[nPeace]

@Jose Fly

Let me ask you this....would you agree that there is evidence that some non-coding regions of DNA are non-functional?

So, chop off a hand, an ear, and a toe.
We are still able to survive, grow, and reproduce. So clearly, they served no functionality. They were useless junk.

Perhaps I'm wrong on that, but I do have to wonder why this subject is of such interest to you. Any particular reason?

I recall I was having a discussion with another poster, so I think if you check back to that conversation, perhaps it would show why the subject came up.

Finally, I noticed you entirely ignored the fact that the work you've been citing is based on the understanding of evolutionary common ancestry between rats, mice, and humans. Care to explain why?

I did not ignore that. Perhaps read again. You might not have grasped my response.

 

[Jose Fly]

So, chop off a hand, an ear, and a toe.
We are still able to survive, grow, and reproduce. So clearly, they served no functionality. They were useless junk.

Ah, but you need to consider the evidence as a whole. So to use your analogy, we would also have to watch people and never once see them using their hands, ears, or toes before we'd conclude that they had no function.

I recall I was having a discussion with another poster, so I think if you check back to that conversation, perhaps it would show why the subject came up.

I will do that. But obviously this topic has generated some level of interest with you...at least enough to continue discussing it with me. Any particular reason why?

I did not ignore that. Perhaps read again. You might not have grasped my response.

Well, it looks like you've gone back and greatly edited your post from earlier today, so I'll pick up from there.

Like I said before, do your research, but to claim you have the "bull by the horns", when you are "grabbing the tail", is a mistake made by some people.
These results, while not inclusive of all the possible phenotypic impact of the deleted sequences, indicate that extreme sequence constraint does not necessarily reflect crucial functions required for viability.
What does this say to you.... that they have sufficient information, so as to be sure?

It's important to understand the larger context of this work. As noted in the paper, Rubin et al. specifically focused on "evolutionarily conserved regions" between the mouse, rat, and human genomes. They selected those regions because, being highly conserved between diverse taxa, geneticists had generally assumed that such regions have a function. Yet when they cut them out they couldn't detect any effects to the organism. As noted in the paper, that was the opposite of what they expected.

So what that statement says to me is that the most logical conclusion is that those sequences are likely non-functional, but it's possible they may indeed have functions. However, even if they do, the functions are so minute and trivial that they are virtually undetectable.

I suggest they are in a dark unfamiliar warehouse, and the lights are not going to come on anytime soon... but they will. I'll wait for the tripping and falling. That's science.

It's fascinating how you have such a dim view of scientists. I'm curious....have you ever worked in a scientific field in any capacity?

I don't see any irony.
When one focuses only on things one has some knowledge of, or familiarity with, it's not difficult to find what one are looking for. That's why a mechanic who never saw a V8 engine can find what he is looking for. Or a computer technician can work on capacitors and other technical parts - although different to ones he worked on previously.
Start with a presumption, and fit all the evidence to it. It should work, so long as you are allowed flexibility.

That's quite an accusation against the scientists. Can you show precisely where they "fit the evidence" to be consistent with evolutionary common descent?

Why do they have to be extra copies?

I'm not sure what you mean here. If they have two copies of the same gene, one gets deleted, and the organism continues to function normally, it's pretty obvious the one that was deleted was extra.

Finally, if you could not do this thing where you go back and add a whole bunch of text and material to a post after I've already replied to it, I would appreciate it greatly. If you think the info is important, just put it in your next post to me. Going back and adding it to an old post that's already been responded to isn't helpful to a conversation.

 

[nPeace]

Ah, but you need to consider the evidence as a whole. So to use your analogy, we would also have to watch people and never once see them using their hands, ears, or toes before we'd conclude that they had no function.

Huh? You lost me. What exactly are you saying?
In the experiment, did they also knock out other regions, resulting in detrimental effects? So let's now cut out a vital organ. Let's see what happens. Oops. We die, or we can't reproduce, or....
More evidence that our hand, ear, and toes are useless junk.

I will do that. But obviously this topic has generated some level of interest with you...at least enough to continue discussing it with me. Any particular reason why?

Why I am discussing it with you? Because you are adamant that you are right, and I know I can show you are wrong. so whether you admit you are wrong or not, I will present the proof that you are wrong.

Well, it looks like you've gone back and greatly edited your post from earlier today, so I'll pick up from there.

Wow. When did I do that, in my sleep?
No. I did no such thing. It looks like you simply are not focused on my arguments, as much as you are focused on your arguments. So you are evidently zipping or skipping through, and not paying attention.

Be back later to address the remainder.

 

[Jose Fly]

Huh? You lost me. What exactly are you saying?

I'm saying that when considering this issue, you should consider the evidence, experimental results, and observations as a whole, rather than all of it being unrelated bits of info.

In the experiment, did they also knock out other regions, resulting in detrimental effects?

No, they did not.

Why I am discussing it with you? Because you are adamant that you are right, and I know I can show you are wrong.

And that's it? It's not anything specific to this subject matter?

Wow. When did I do that, in my sleep?
No. I did no such thing.

Okay then. I just don't recall seeing all that other material when I clicked "reply". It may be that you were editing it as I was replying to it.

Be back later to address the remainder.

No worries.

 

[nPeace]

It's important to understand the larger context of this work. As noted in the paper, Rubin et al. specifically focused on "evolutionarily conserved regions" between the mouse, rat, and human genomes. They selected those regions because, being highly conserved between diverse taxa, geneticists had generally assumed that such regions have a function. Yet when they cut them out they couldn't detect any effects to the organism. As noted in the paper, that was the opposite of what they expected.

Thank you. This is what can happen when one makes assumptions.
Maybe you do not grasp what this implies. First, they assumed - you admit that part (we don't need Sherlock Holmes here to tell us why you admit that part so willingly). So here is the thing.... Why did they assume? They don't know. Okay.

So they cut out those parts, and now what? They know they don't have function?
No they don't They once again assume, only this is the part you have not admitted.

Aside from the fact that Ruben admitted it (when he mentioned two possibilities one must take into account), there is the analogy I used - they assumed that the parts they cut out are of no use, just because they saw no significant change in a few "traits" of the organism... when in effect those parts may be important for other functions, while not of significant necessity for the functions examined.
According to researchers... All Conserved non-coding sequences are likely to perform some function in order to have constraints on their evolution, but they can be distinguished based on where in the genome they are found and how they got there.

So what that statement says to me is that the most logical conclusion is that those sequences are likely non-functional, but it's possible they may indeed have functions. However, even if they do, the functions are so minute and trivial that they are virtually undetectable.

Thank you for acknowledging that your conclusion is not based on sufficient information, and therefore being unsure, is considered an assumption... even if you don't like to use the word, at the times when you want to argue strongly, for your opinion.
Yes. That's the truth. Your conclusion is an opinion that is not conclusive.
Unfortunately, you make another assumption - that any "functions are so minute and trivial". Wow. I'm not even going to ask how you know that.

It's fascinating how you have such a dim view of scientists. I'm curious....have you ever worked in a scientific field in any capacity?

A dim view of scientists? That doesn't seem an accurate assessment.
I can give you another perspective - one you might not be familiar with. How about this. Some people have more than an elevated view of themselves. Some scientist are humble. I like the latter kind.

Scientists are human... I hope, and therefore they are not free from having an unrealistic and biased view. Nor are they exempt from being pig-headed.
Pig-headed scientists
"Scientists, especially when they leave the particular field in which they have specialized, are just as ordinary, pig-headed and unreasonable as anybody else, and their unusually high intelligence only makes their prejudices all the more dangerous..."
Eysenck, H.J. (1957) Sense and nonsense in psychology.

I am not going to answer the question though, since it appears to be one of two types of questions - the fishing type, or the character assassination type.
If it's the latter, that would characterize a mentality, of people who wear their credentials like a badge.
Have you ever watched those old Western Cowboy movies, where the sheriff walks around town and goes...

Ain't nobody gonna forget that.
Hopefully, your question is of the first type.
If you are just fishing, you might be doing so in the wrong waters.

I don't want to quote mine all the scientists who agree that some research takes them into deep darkness, where 'they have to feel around in the dark, and sometimes bump against things they make assumptions about, and sometimes trip and fall over other things'.
If you want me to quote them, I'd be happy to make that a project. Just let me know.

You can however, read the first paragraph in this article - Shedding Light on the Genome’s Dark Matter.

That's quite an accusation against the scientists. Can you show precisely where they "fit the evidence" to be consistent with evolutionary common descent?

Yes I can, but that's a lot, and it will take me a few days to put all of it together.
You can listen to the podcast though. There is a little of it there.

I'm not sure what you mean here. If they have two copies of the same gene, one gets deleted, and the organism continues to function normally, it's pretty obvious the one that was deleted was extra.

Did you say "was extra"?
Well pardon me. That sounds quite different to "Yep, which would mean the extra copies are just that....extra."
What did you mean by that statement?

Finally, if you could not do this thing where you go back and add a whole bunch of text and material to a post after I've already replied to it, I would appreciate it greatly. If you think the info is important, just put it in your next post to me. Going back and adding it to an old post that's already been responded to isn't helpful to a conversation.

I never did that. If you paid attention, that might help solve that problem.
I think you assumed I made one post, and therefore you paid no attention to what was above it.
I posted both together, because I had to split the post in two, since it exceeded the length allowed by RF.
If I edited anything, it was probably a typo, in one word.

I'm saying that when considering this issue, you should consider the evidence, experimental results, and observations as a whole, rather than all of it being unrelated bits of info.

I still don't understand how I didn't do that

No, they did not.

Okay. They just knocked out surrounding genes they were familiar with, that cause problems. To prove what... that they can kill the mice?
I wonder if the animal rights activists are reading science journals.

And that's it? It's not anything specific to this subject matter?

What do you mean by this subject matter? I remember I was discussing evolution theory, and someone was directing my attention to pseudogenes as proof. That's when I brought in junk DNA.

Okay then. I just don't recall seeing all that other material when I clicked "reply". It may be that you were editing it as I was replying to it.

The only thing I recall editing was this... That does not mean that all of it is non-functional, where I added non- to functional. That's all.

No worries.

Right.

 

[Jose Fly]

Thank you. This is what can happen when one makes assumptions.
Maybe you do not grasp what this implies. First, they assumed - you admit that part (we don't need Sherlock Holmes here to tell us why you admit that part so willingly). So here is the thing.... Why did they assume? They don't know. Okay.

So they cut out those parts, and now what? They know they don't have function?
No they don't They once again assume, only this is the part you have not admitted.

Again, all I can do is repeat what I've said.....Rubin and his colleagues did indeed "assume" that the sequences in question were functional (because they were conserved across rats, mice, and humans). But they didn't just assume and stop there, did they? They went out and conducted research specifically designed to test that assumption, and ended up getting results they didn't expect (the sequences were not meaningful to the fitness or survival of the mice).

That's how science works.

Aside from the fact that Ruben admitted it (when he mentioned two possibilities one must take into account), there is the analogy I used - they assumed that the parts they cut out are of no use, just because they saw no significant change in a few "traits" of the organism... when in effect those parts may be important for other functions, while not of significant necessity for the functions examined.

All I can do is repeat what I said earlier. You seem to be extremely determined to categorize the conclusions of scientific research as "assumption". Why, only you can say.

For most folks OTOH, there is a big difference between geneticists "assuming" that non-coding DNA is non-functional and them "concluding" that it is non-functional. If I tell people about the types of research, experiments, and study that's gone into this subject and asked them whether it's more accurate to say the scientists merely assumed, or whether they reached conclusions, what do you think most people would say?

According to researchers... All Conserved non-coding sequences are likely to perform some function in order to have constraints on their evolution, but they can be distinguished based on where in the genome they are found and how they got there.

And I would generally agree with that, since it's specific to conserved non-coding sequences. That's why Rubin expressed surprise at his results in the mice knock-out experiments. As I noted earlier, the "assumption" that he started with was that the conserved regions are functional, but the results of his experiment caused him to rethink that assumption.

Also, again we can see how an understanding of evolutionary relatedness serves as the basis for this entire field of study, by telling them which genomes to compare, where to look, and what to look for. Without that understanding, none of the work you've been citing would even be possible.

Thank you for acknowledging that your conclusion is not based on sufficient information, and therefore being unsure, is considered an assumption... even if you don't like to use the word, at the times when you want to argue strongly, for your opinion.
Yes. That's the truth. Your conclusion is an opinion that is not conclusive.

Again I notice that you're really trying hard to spin the process of deriving conclusions from research as "assuming". Why, only you can say.

Unfortunately, you make another assumption - that any "functions are so minute and trivial". Wow. I'm not even going to ask how you know that.

Because the results of the experiment show that mice lacking those segments are just as fit and normal as the non-knock-out mice. If you disagree with my conclusion, what makes you think those sequences are vital and important to the survival and fitness of the organism?

I am not going to answer the question though, since it appears to be one of two types of questions - the fishing type, or the character assassination type.

That's okay, I was just curious.

You can however, read the first paragraph in this article - Shedding Light on the Genome’s Dark Matter.

Thanks. As I noted earlier, there are certainly some types of non-coding sequences that you definitely don't want to become functional.

Yes I can, but that's a lot, and it will take me a few days to put all of it together.

I will be expecting it.

Did you say "was extra"?
Well pardon me. That sounds quite different to "Yep, which would mean the extra copies are just that....extra."
What did you mean by that statement?

If an organism has one original gene and a second copy of that gene, and you remove the copy and the organism shows no effect, that indicates that the second was an extra copy. ("was" is past tense because the organism no longer has it)

I never did that. If you paid attention, that might help solve that problem.

It's okay. You edited the post 10 minutes after first posting it. I had already started replying to it while you were editing it.

I still don't understand how I didn't do that

My suggestion is that you approach this like a jigsaw puzzle. It's only when you put all the pieces together that the full picture emerges.

Okay. They just knocked out surrounding genes they were familiar with, that cause problems. To prove what... that they can kill the mice?
I wonder if the animal rights activists are reading science journals.

Sorry, I'm not following you here. To recap, the researchers utilized their understanding of the evolutionary relationships between rats, mice, and humans to identify specific segments of non-coding DNA that were identical across all three species. Because the segments were conserved, they figured they must serve a function (otherwise they would have mutated into nonsense). So to test that, they bred mice that were lacking those segments and it turns out the mice were completely normal, thereby leading to the conclusion that those specific segments are either non-functional, or perform a minute and non-essential function.

What do you mean by this subject matter? I remember I was discussing evolution theory, and someone was directing my attention to pseudogenes as proof. That's when I brought in junk DNA.

I mean the subject of "junk DNA". Is the prospect of non-functional DNA concerning to you in any way? Do you have an interest in one specific outcome?

 

[nPeace]

Again, all I can do is repeat what I've said.....Rubin and his colleagues did indeed "assume" that the sequences in question were functional (because they were conserved across rats, mice, and humans). But they didn't just assume and stop there, did they? They went out and conducted research specifically designed to test that assumption, and ended up getting results they didn't expect (the sequences were not meaningful to the fitness or survival of the mice).

That's how science works.


All I can do is repeat what I said earlier. You seem to be extremely determined to categorize the conclusions of scientific research as "assumption". Why, only you can say.

For most folks OTOH, there is a big difference between geneticists "assuming" that non-coding DNA is non-functional and them "concluding" that it is non-functional. If I tell people about the types of research, experiments, and study that's gone into this subject and asked them whether it's more accurate to say the scientists merely assumed, or whether they reached conclusions, what do you think most people would say?


And I would generally agree with that, since it's specific to conserved non-coding sequences. That's why Rubin expressed surprise at his results in the mice knock-out experiments. As I noted earlier, the "assumption" that he started with was that the conserved regions are functional, but the results of his experiment caused him to rethink that assumption.

Also, again we can see how an understanding of evolutionary relatedness serves as the basis for this entire field of study, by telling them which genomes to compare, where to look, and what to look for. Without that understanding, none of the work you've been citing would even be possible.


Again I notice that you're really trying hard to spin the process of deriving conclusions from research as "assuming". Why, only you can say.


Because the results of the experiment show that mice lacking those segments are just as fit and normal as the non-knock-out mice. If you disagree with my conclusion, what makes you think those sequences are vital and important to the survival and fitness of the organism?

The results did not show that, now, did they?
Was this your comment?
...even if they do, the functions are so minute and trivial that they are virtually undetectable.

First. You acknowledged that it's possible they do have function. Why? Because the experiment did not prove otherwise. If it did, there would be no need to consider any possibility that they do. Correct?

Would your comment have been made without considering the factors contributing to those possibilities?
1. The experimental setup could have missed phenotypic changes that may have emerged under other conditions
2. Because the regions of DNA were chosen based on their ability to promote transcription in lab tests - that is, the elements were capable of function. It is possible that deleting them produced no obvious effects, because other elements stepped in to perform their job.

So you have no way of knowing if the mice were indeed lacking those segments. Isn't that true?

That's okay, I was just curious.


Thanks. As I noted earlier, there are certainly some types of non-coding sequences that you definitely don't want to become functional.


I will be expecting it.

Don't. I don't feel like. Perhaps I will just give you bit by bit, as I move along in the other thread. We'll see how that goes. So far we seem stalled there.

If an organism has one original gene and a second copy of that gene, and you remove the copy and the organism shows no effect, that indicates that the second was an extra copy. ("was" is past tense because the organism no longer has it)

True, but what does that have to do with making a backup copy of a gene when needed, as the original is being removed.
Windows OS does not anticipate that you will delete a file, and make a copy and store it. Otherwise, you would be wondering why your drive space is missing double the amount of memory for all your files.
The "copy" (it really isn't a copy), is made, when you confirm deletion.
So the backup copy of the gene, is there, only after deleting the original. Otherwise, there is no extra. Not even after, there is no extra. There was only an extra moments before the original was deleted.

It's okay. You edited the post 10 minutes after first posting it. I had already started replying to it while you were editing it.


My suggestion is that you approach this like a jigsaw puzzle. It's only when you put all the pieces together that the full picture emerges.


Sorry, I'm not following you here. To recap, the researchers utilized their understanding of the evolutionary relationships between rats, mice, and humans to identify specific segments of non-coding DNA that were identical across all three species. Because the segments were conserved, they figured they must serve a function (otherwise they would have mutated into nonsense). So to test that, they bred mice that were lacking those segments and it turns out the mice were completely normal, thereby leading to the conclusion that those specific segments are either non-functional, or perform a minute and non-essential function.

I'm not referring to that.
I am referring to the section under the subheading Screens for Phenotypes of Adjacent Genes

I mean the subject of "junk DNA". Is the prospect of non-functional DNA concerning to you in any way? Do you have an interest in one specific outcome?

I'm not following your line of questioning.
You can follow our conversation from here, if you don't remember what this is about.

 

[Jose Fly]

The results did not show that, now, did they?

Sure they did. Rubin et al. even said so in the paper you linked to below (last sentence in the Discussion section)...

"While our studies have not defined a specific need for the extreme sequence constraints of noncoding ultraconserved elements, they have ruled out the hypothesis that these constraints reflect crucial functions required for viability."​

I agree. We can definitely rule out the notion that the knocked-out sequences have a vital function.

Was this your comment?
...even if they do, the functions are so minute and trivial that they are virtually undetectable.

First. You acknowledged that it's possible they do have function. Why? Because the experiment did not prove otherwise. If it did, there would be no need to consider any possibility that they do. Correct?

Would your comment have been made without considering the factors contributing to those possibilities?
1. The experimental setup could have missed phenotypic changes that may have emerged under other conditions
2. Because the regions of DNA were chosen based on their ability to promote transcription in lab tests - that is, the elements were capable of function. It is possible that deleting them produced no obvious effects, because other elements stepped in to perform their job.

Yes, all those are possible.

Let me see if I can explain it this way.....It's a lot like concluding that there's no life on the moon. Can we ever say with 100% absolute certainty that there isn't? No matter what we do, isn't there always the possibility that we've overlooked something, or that life forms are deep underground, or that they're so unique we wouldn't recognize them if we found them, or that they're invisible, or that......well, you get the idea.

No matter what we do, we can never say with 100% absolute certainty "There is no life on the moon".

However after we've been there a few times and looked around and conducted all manner of tests, we can say with a high degree of confidence "There is no life on the moon". Does that make sense?

So you have no way of knowing if the mice were indeed lacking those segments. Isn't that true?

If you're referring to the conserved segments that were knocked out, yes we know for a fact that the mice lack those segments (because the geneticists removed them).

Don't. I don't feel like. Perhaps I will just give you bit by bit, as I move along in the other thread. We'll see how that goes. So far we seem stalled there.

I expect that if you're going to make such a serious accusation against a group of people, you would feel at least some moral obligation to back up that accusation. You wouldn't like it if people made empty accusations against you, would you?

True, but what does that have to do with making a backup copy of a gene when needed, as the original is being removed.
Windows OS does not anticipate that you will delete a file, and make a copy and store it. Otherwise, you would be wondering why your drive space is missing double the amount of memory for all your files.
The "copy" (it really isn't a copy), is made, when you confirm deletion.
So the backup copy of the gene, is there, only after deleting the original. Otherwise, there is no extra. Not even after, there is no extra. There was only an extra moments before the original was deleted.

Actually, the copies are already there before any deletion occurs. Parts of genomes copy themselves very regularly, so much so that about two-thirds of the human genome is made up of repeats/copies.

So specific to our discussion, the point was that if an organism has two versions of a gene (one original and one copy), if you delete one of them the other can take over. And to reiterate, the organism doesn't make an extra copy as the old one is deleted. The copy is already there.

I'm not referring to that.
I am referring to the section under the subheading Screens for Phenotypes of Adjacent Genes

Okay, thanks for clarifying.

The point there is that the geneticists wanted to see if the conserved segments they were deleting served a regulatory function for the genes adjacent to the conserved segments. So they first had to establish what those adjacent genes did in the mice; one way to do that is to delete those adjacent genes and see what happens. They deleted the adjacent genes and documented the effects (which were very bad for the mice).

For example, one of the adjacent genes plays a role in eye development. So after they knock out the conserved segments, if they see the mice have problems with eye development they'll know that at least one of the functions of the conserved regions is regulation of the adjacent gene that plays a role in eye development. But since the knock-out mice showed no such ill effects, we can rule out the possibility that the conserved elements regulate the adjacent genes.

I'm not following your line of questioning.
You can follow our conversation from here, if you don't remember what this is about.

I'm just wondering if the prospect of non-functional DNA is problematic for you. IOW, are you okay with the existence of "junk DNA"?

 

[nPeace]

Sure they did. Rubin et al. even said so in the paper you linked to below (last sentence in the Discussion section)...

"While our studies have not defined a specific need for the extreme sequence constraints of noncoding ultraconserved elements, they have ruled out the hypothesis that these constraints reflect crucial functions required for viability."​

I agree. We can definitely rule out the notion that the knocked-out sequences have a vital function.


Yes, all those are possible.

Let me see if I can explain it this way.....It's a lot like concluding that there's no life on the moon. Can we ever say with 100% absolute certainty that there isn't? No matter what we do, isn't there always the possibility that we've overlooked something, or that life forms are deep underground, or that they're so unique we wouldn't recognize them if we found them, or that they're invisible, or that......well, you get the idea.

No matter what we do, we can never say with 100% absolute certainty "There is no life on the moon".

However after we've been there a few times and looked around and conducted all manner of tests, we can say with a high degree of confidence "There is no life on the moon". Does that make sense?

So do you agree that the conclusion that there is no life on the moon is based on an inability to gain sufficient information at this time? Therefore you cannot be sure?
Another example... What is the conclusion about Dark Energy?
It's not dismissed as nothing just because they don't know what it is, or if it is having the effect they assume. They wait until they can gather more data. Perhaps their instruments are a bit lacking right now.

Likewise, the experiment was not sufficient to rule out other factors. Therefore the researchers, who recognize what true science involves do not follow the example that gets some scientists, the label "pig-headed". Rather, they take the attitude that future studies can explore these possibilities and continue to probe the mechanisms that gave rise to such extreme evolutionary conservation.

If you're referring to the conserved segments that were knocked out, yes we know for a fact that the mice lack those segments (because the geneticists removed them).
Those particular copies, yes. Copies of them, no.

I expect that if you're going to make such a serious accusation against a group of people, you would feel at least some moral obligation to back up that accusation. You wouldn't like it if people made empty accusations against you, would you?
I made no empty accusations. I gave you a start, and said I may give you other pieces later.

Actually, the copies are already there before any deletion occurs. Parts of genomes copy themselves very regularly, so much so that about two-thirds of the human genome is made up of repeats/copies.

So specific to our discussion, the point was that if an organism has two versions of a gene (one original and one copy), if you delete one of them the other can take over. And to reiterate, the organism doesn't make an extra copy as the old one is deleted. The copy is already there.

I don't know, honestly.

Okay, thanks for clarifying.

The point there is that the geneticists wanted to see if the conserved segments they were deleting served a regulatory function for the genes adjacent to the conserved segments. So they first had to establish what those adjacent genes did in the mice; one way to do that is to delete those adjacent genes and see what happens. They deleted the adjacent genes and documented the effects (which were very bad for the mice).

For example, one of the adjacent genes plays a role in eye development. So after they knock out the conserved segments, if they see the mice have problems with eye development they'll know that at least one of the functions of the conserved regions is regulation of the adjacent gene that plays a role in eye development. But since the knock-out mice showed no such ill effects, we can rule out the possibility that the conserved elements regulate the adjacent genes.

I'm just wondering if the prospect of non-functional DNA is problematic for you. IOW, are you okay with the existence of "junk DNA"?

Actually, I connected the dots. Tell me if I got it right, or if I am wrong.
You want to know if this is in some way related to my religious beliefs. Right or wrong?

 

[Jose Fly]

So do you agree that the conclusion that there is no life on the moon is based on an inability to gain sufficient information at this time? Therefore you cannot be sure?

Not at all. There's a reason no one is sending probes and such to the moon to look for life....we already know with a high degree of certainty that life isn't there. Similarly, we know with a high degree of certainty that parts of the human genome (and the genomes of other organisms) are non-functional. In both cases there is always a possibility that we've missed something, but that possibility is so remote that it doesn't warrant serious consideration.

Another example... What is the conclusion about Dark Energy?
It's not dismissed as nothing just because they don't know what it is, or if it is having the effect they assume. They wait until they can gather more data. Perhaps their instruments are a bit lacking right now.

I honestly know very little about that subject.

Likewise, the experiment was not sufficient to rule out other factors.

Again, just like with life on the moon, we can never rule out absolutely everything imaginable. The very best we'll ever be able to do is what I've been saying....reach conclusions with a very high degree of certainty.

Therefore the researchers, who recognize what true science involves do not follow the example that gets some scientists, the label "pig-headed". Rather, they take the attitude that future studies can explore these possibilities and continue to probe the mechanisms that gave rise to such extreme evolutionary conservation.

Yep. Specific to ultra-conserved elements (which again we only discovered via application of evolutionary common ancestry), it is a very interesting question.

I made no empty accusations.

So let's clarify. When I first pointed out to you the fact that evolutionary common ancestry was the means by which the ultra-conserved elements were even discovered, you responded, "Start with a presumption, and fit all the evidence to it". What did you mean by that? Who specifically do you think manipulated the data to fit a presumption?

I don't know, honestly.

I'm not sure what you're referring to. What don't you know?

Actually, I connected the dots. Tell me if I got it right, or if I am wrong.
You want to know if this is in some way related to my religious beliefs. Right or wrong?

Perhaps, but that's not really important right now. My main curiosity at this point is why you seem to be coming into this with a pre-held position that "junk DNA" doesn't exist.

 

[nPeace]

Not at all. There's a reason no one is sending probes and such to the moon to look for life....we already know with a high degree of certainty that life isn't there. Similarly, we know with a high degree of certainty that parts of the human genome (and the genomes of other organisms) are non-functional. In both cases there is always a possibility that we've missed something, but that possibility is so remote that it doesn't warrant serious consideration.

What has led to that high degree of certainty, besides the fact that they know it is highly unlikely, because LUCA is highly unlikely... imo.

I honestly know very little about that subject.


Again, just like with life on the moon, we can never rule out absolutely everything imaginable. The very best we'll ever be able to do is what I've been saying....reach conclusions with a very high degree of certainty.

Reach conclusions with a high level of uncertainty, but consider it a high degree of certainty.

Yep. Specific to ultra-conserved elements (which again we only discovered via application of evolutionary common ancestry), it is a very interesting question.

Pardon me? What are you responding to?

So let's clarify. When I first pointed out to you the fact that evolutionary common ancestry was the means by which the ultra-conserved elements were even discovered, you responded, "Start with a presumption, and fit all the evidence to it". What did you mean by that? Who specifically do you think manipulated the data to fit a presumption?

What don't you understand from that?

I'm not sure what you're referring to. What don't you know?

I don't know when exactly copies are made, or not made.

Perhaps, but that's not really important right now. My main curiosity at this point is why you seem to be coming into this with a pre-held position that "junk DNA" doesn't exist.

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"

 

[gnostic]

So, chop off a hand, an ear, and a toe.
We are still able to survive, grow, and reproduce. So clearly, they served no functionality. They were useless junk.

Wrong.each one of them have functions, so they are not useless and they are not junk.

Just because your example showed that they can survive without them, it doesn’t mean they have no function.

And none of your example have anything to do with Evolution.

For instance. If you were to cut off someone’s right hand off, like losing it in some sort of accident. Should that person have children, then if it was evolution, then each child would be born with missing right hand.

That’s not how Evolution works.

A person losing a hand and survive, doesn’t mean it is Evolution.

And a hand lost due to accident or by intention, won’t mean that person will have children and descendants, will be born with missing right hands.