I’m not an expert on the subject. I can only repeat what Venter said: “the only junk DNA is in my colleagues brains”. He claims that all DNA has function and that it should not be referred to as junk just because we don’t know the function yet.
He needs to look at some plant DNA, there are places with 50 times now DNA codons per cell than Humans have, with many many many times fewer genes.
“If it’s there it must be there for a reason” sounds an awful lot like intelligent design to me, and his putting down his colleges for holding alternative (seemingly more informed than his own) theories doesn’t help my view of him. More codons don’t mean more reason, evolution is not what is most efficient, it’s just what works best at any time. It’s also full of cross contamination at the simple life form level, and what’s good for one single cellular life form might benefit another life form, but the entirety of that first life form isn’t necessary for the second, so evolution would suggest that the absorbing life form will slowly whittle down what isn’t necessary.
Or has mitochondria always been perfectly fit for it’s function in our cells? (Hint it hasn’t)
I don’t think that Venter is suggesting intelligent design. He’s claiming, as a result of his research, that it’s not effective to assume simple explanations for genomics and especially for cellular biology.
Every technological improvement in the methods of research has revealed more complexity in organisms and so it behooves us to suspend dogmatic approaches to the genome. That’s the subject of the book discussed in the article.
Craig Venter is very controversial and his statements are provocative. I’m not qualified to critique the science in this field. But I’d recommend you to take a look at the work his team is doing with synthetic chromosomes and engineered cells.
‘Junk DNA’ is any DNA whose purpose was unknown when the article / book was written. But to return to your question, not necessarily.
First, we are usually concerned with the (dis)advantages of mutations when they occur in coding regions, which are definitely not junk DNA.
Second, just because a sequence does not encode any useful information does not mean it is useless. For example, it could be holding a coding region away from another, so both can be transcribed at the same time. Or it could be structurally important in the way the chromosome is folded.
I don’t know too much about the subject, but maybe this almost 30 year old article can help. There’s more specific examples in the article, but this quote captures the direction:
“I don’t believe in junk DNA,” said Dr. Walter Gilbert of Harvard University, a pre-eminent theoretician of the human genome. “I’ve long believed that the attitude that all information is contained in the coding regions is very shortsighted, reflecting a protein chemist’s bias of looking at DNA.” Coding regions may make the proteins that are dear to a chemist’s heart; but true biologists, he added, know that much of the exquisite control over these proteins is held offstage, nested within the noncoding junk.
There are plenty of plants that execute the exact same functions with code thousands of times smaller.
To say every codon has a purpose is to be ignorant of how evolution works. There are start triplicate pairs and stop triplicate pairs, the regions between stop and start don’t need to have function, even structurally, otherwise why would chromosomes come in different lengths? There was no creator of the genome, there was no efficiency driven outcome, there’s only descent with modification, things just happen to with the way they work, and that’s beautiful in it’s own way.
Again, and I can’t emphasize this enough, this is not my area of study and seems like you have better handling of the subject. But when I read his quote, this part sticks out to me:
much of the exquisite control over these proteins is held offstage, nested within the noncoding junk.
Additionally, the article calls into question the role of code and protein production as the only role for DNA.
Still other noncoding stretches may be buffers against precipitous change, serving rather as flak jackets to absorb the impact of viruses and other genetic interlopers that infiltrate an animal’s chromosomes. Without all the extra padding to absorb the blows, viruses or the bizarre genetic sequences that hop and skip from one part of the chromosome to another – mysterious genetic elements called transposons or jumping genes – might land smack in the middle of a crucial gene, disrupting its performance.
So there maybe stretches of DNA that don’t participate in protein construction, but still has a role. So I question I idea of centering one type function over another.
@TempermentalAnomaly@morphballganon
Junk dna was junk science from the start for ignoring that evolution often eliminates or reduces useless things, like eyes in cave fish, so there’s little likelihood that there’s useless parts of the genome.
But it doesn’t do that instantly and it does it for good reason, eyes and the sections of the brain using them require energy and are vulnerable to infection so in situations where they don’t provide an advantage they increase the likelihood of death before breeding thus giving any offspring born with less energy devoted to eyes has a small advantage which over s very long time results in them being selected away.
So unless the creatures reach a perfect form for their environment then they’ll always be in the process of changing and have some of the old junk in there. Also if the formerly useful part doesn’t make any real difference to survivability there’s no force driving it to be selected away from, it might eventually be removed by lots of pure chance events but that’s going to take a huge amount of generations meaning the middle time where there’s junk not yet removed us going to be very long
Junk DNA is repeating codons, or codons that occur in areas that are outside of the “start/stop” codon triplicate pairs. A DNA transcribing protein will read the genetic code from a start signal, until it gets to a stop signal. Then it clips itself off the chain and re-binds the chain together for the next transcriber to use. Sometimes there are extra codons between a stop signal and the next start signal, sometimes there are hundreds of thousands of extra codons. They aren’t there for structural reasons, all DNA is the same 4 codons linked together over and over, all the different chromosomes are different sizes. All of this DNA is reported when the cells divide, that’s the only time those regions between the stops and starts actually come into play. This is very easily proven, we know the structure of the reading proteins down to the molecule (indeed there are starts and stops and triplicate base pairs that design these transcribing proteins). The “important” junk DNA that has significance while not being in a “start->stop” zone are the codons that occur before the first start codon on either side of a DNA strand, when DNA is replicated the protein that starts replicating it has to start at 1 end of 1 side of the DNA in order to be able to read it, except it needs to find the end first, and to make sure it’s all the end it “clips” the first 6 (? Maybe more maybe less, it’s been decades since I’ve studied this) codons from the strand of DNA, this is lost for all future replications of the cell, your DNA actually gets shorter every time your cells reproduce (except your miosis division cells, they have a special replication process that keeps the full length of every chromosome).
Sorry for the wall of text, but there’s plenty of examples of blatantly junk DNA, and there are known methods of how it occurs. Anyone who says every codon pair has a purpose has a screw loose and is ignorant to the mechanics of evolution.
Junk DNA is repeating codons, or codons that occur in areas that are outside of the “start/stop” codon triplicate pairs.
Those sequences do things and have effects. In fact, the coding regions are often less functional than the non-coding ones.
They aren’t there for structural reasons, all DNA is the same 4 codons linked together over and over, all the different chromosomes are different sizes.
Sometimes they ARE there for structural reasons? Read: enhancers, or CTCF binding sites? Among many other myriad examples of functional noncoding regions? Also, nucleotides =/= codons. There are 64 codons.
All of this DNA is reported when the cells divide, that’s the only time those regions between the stops and starts actually come into play. This is very easily proven, we know the structure of the reading proteins down to the molecule (indeed there are starts and stops and triplicate base pairs that design these transcribing proteins).
That’s bull. You’re out of your depth. A contemporary college molecular biology course would show your examples to the contrary.
The “important” junk DNA that has significance while not being in a “start->stop” zone are the codons that occur before the first start codon on either side of a DNA strand, when DNA is replicated the protein that starts replicating it has to start at 1 end of 1 side of the DNA in order to be able to read it
I feel like a broken record but Enhancers! lncRNAs! siRNAs! Binding sites! Other gene regulatory regions! Epigenetic nucleosome modifications! Chromatin remodeler sites!
except it needs to find the end first, and to make sure it’s all the end it “clips” the first 6 (? Maybe more maybe less, it’s been decades since I’ve studied this)
Oh, there’s your problem. A lot has changed. You refuse to see the sea change happening around you because it means you’re out of date.
Sorry for the wall of text, but there’s plenty of examples of blatantly junk DNA, and there are known methods of how it occurs. Anyone who says every codon pair has a purpose has a screw loose and is ignorant to the mechanics of evolution.
I was happy to reply to you and engage pleasantly originally but you are only engaging with people that know less about biology than you do. You are not an expert if you last studied biology decades ago and can’t remember the details. You certainly aren’t enough of an authority on the subject to question a contemporary article published in Science or the work of other researchers currently in the field.
I really, really encourage you to read these papers thoroughly. You are the target audience-- people who learned the machine model of the cell and who are gripping it so tightly that they are blind to the nuance that we’ve uncovered. I also encourage you to not write insults about people who disagree with you, especially people with more domain knowledge than you have.
Every sperm isn’t sacred and every piece of DNA isn’t with purpose, otherwise explain ferns and plants having hundreds of times more DNA than higher functioning life forms.
I’m not an expert on the subject. I can only repeat what Venter said: “the only junk DNA is in my colleagues brains”. He claims that all DNA has function and that it should not be referred to as junk just because we don’t know the function yet.
He talks about at intervals in this interview.
He needs to look at some plant DNA, there are places with 50 times now DNA codons per cell than Humans have, with many many many times fewer genes.
“If it’s there it must be there for a reason” sounds an awful lot like intelligent design to me, and his putting down his colleges for holding alternative (seemingly more informed than his own) theories doesn’t help my view of him. More codons don’t mean more reason, evolution is not what is most efficient, it’s just what works best at any time. It’s also full of cross contamination at the simple life form level, and what’s good for one single cellular life form might benefit another life form, but the entirety of that first life form isn’t necessary for the second, so evolution would suggest that the absorbing life form will slowly whittle down what isn’t necessary.
Or has mitochondria always been perfectly fit for it’s function in our cells? (Hint it hasn’t)
I don’t think that Venter is suggesting intelligent design. He’s claiming, as a result of his research, that it’s not effective to assume simple explanations for genomics and especially for cellular biology.
Every technological improvement in the methods of research has revealed more complexity in organisms and so it behooves us to suspend dogmatic approaches to the genome. That’s the subject of the book discussed in the article.
Craig Venter is very controversial and his statements are provocative. I’m not qualified to critique the science in this field. But I’d recommend you to take a look at the work his team is doing with synthetic chromosomes and engineered cells.
If there is a random mutation that is neither advantageous nor disadvantageous, wouldn’t that be junk DNA?
Are we going to say we need to see how every descendant of the creature fares before we can decide whether it was junk DNA or not?
‘Junk DNA’ is any DNA whose purpose was unknown when the article / book was written. But to return to your question, not necessarily.
First, we are usually concerned with the (dis)advantages of mutations when they occur in coding regions, which are definitely not junk DNA.
Second, just because a sequence does not encode any useful information does not mean it is useless. For example, it could be holding a coding region away from another, so both can be transcribed at the same time. Or it could be structurally important in the way the chromosome is folded.
I don’t know too much about the subject, but maybe this almost 30 year old article can help. There’s more specific examples in the article, but this quote captures the direction:
A pretty deus ex machina approach.
How would the size of this plants genetic code be justified I wonder?
https://en.m.wikipedia.org/wiki/Paris_japonica
There are plenty of plants that execute the exact same functions with code thousands of times smaller.
To say every codon has a purpose is to be ignorant of how evolution works. There are start triplicate pairs and stop triplicate pairs, the regions between stop and start don’t need to have function, even structurally, otherwise why would chromosomes come in different lengths? There was no creator of the genome, there was no efficiency driven outcome, there’s only descent with modification, things just happen to with the way they work, and that’s beautiful in it’s own way.
Again, and I can’t emphasize this enough, this is not my area of study and seems like you have better handling of the subject. But when I read his quote, this part sticks out to me:
Additionally, the article calls into question the role of code and protein production as the only role for DNA.
So there maybe stretches of DNA that don’t participate in protein construction, but still has a role. So I question I idea of centering one type function over another.
@TempermentalAnomaly @morphballganon
Junk dna was junk science from the start for ignoring that evolution often eliminates or reduces useless things, like eyes in cave fish, so there’s little likelihood that there’s useless parts of the genome.
But it doesn’t do that instantly and it does it for good reason, eyes and the sections of the brain using them require energy and are vulnerable to infection so in situations where they don’t provide an advantage they increase the likelihood of death before breeding thus giving any offspring born with less energy devoted to eyes has a small advantage which over s very long time results in them being selected away.
So unless the creatures reach a perfect form for their environment then they’ll always be in the process of changing and have some of the old junk in there. Also if the formerly useful part doesn’t make any real difference to survivability there’s no force driving it to be selected away from, it might eventually be removed by lots of pure chance events but that’s going to take a huge amount of generations meaning the middle time where there’s junk not yet removed us going to be very long
@Meowoem
Agree that genome reduction is the slower process, but it’s part of genome evolution, not only the more “energetically expensive” parts.
“Quantitatively, the evolution of genomes appears to be dominated by reduction and simplification, punctuated by episodes of complexification.”
https://onlinelibrary.wiley.com/doi/10.1002/bies.201300037
Junk DNA is repeating codons, or codons that occur in areas that are outside of the “start/stop” codon triplicate pairs. A DNA transcribing protein will read the genetic code from a start signal, until it gets to a stop signal. Then it clips itself off the chain and re-binds the chain together for the next transcriber to use. Sometimes there are extra codons between a stop signal and the next start signal, sometimes there are hundreds of thousands of extra codons. They aren’t there for structural reasons, all DNA is the same 4 codons linked together over and over, all the different chromosomes are different sizes. All of this DNA is reported when the cells divide, that’s the only time those regions between the stops and starts actually come into play. This is very easily proven, we know the structure of the reading proteins down to the molecule (indeed there are starts and stops and triplicate base pairs that design these transcribing proteins). The “important” junk DNA that has significance while not being in a “start->stop” zone are the codons that occur before the first start codon on either side of a DNA strand, when DNA is replicated the protein that starts replicating it has to start at 1 end of 1 side of the DNA in order to be able to read it, except it needs to find the end first, and to make sure it’s all the end it “clips” the first 6 (? Maybe more maybe less, it’s been decades since I’ve studied this) codons from the strand of DNA, this is lost for all future replications of the cell, your DNA actually gets shorter every time your cells reproduce (except your miosis division cells, they have a special replication process that keeps the full length of every chromosome).
Sorry for the wall of text, but there’s plenty of examples of blatantly junk DNA, and there are known methods of how it occurs. Anyone who says every codon pair has a purpose has a screw loose and is ignorant to the mechanics of evolution.
Those sequences do things and have effects. In fact, the coding regions are often less functional than the non-coding ones.
Sometimes they ARE there for structural reasons? Read: enhancers, or CTCF binding sites? Among many other myriad examples of functional noncoding regions? Also, nucleotides =/= codons. There are 64 codons.
That’s bull. You’re out of your depth. A contemporary college molecular biology course would show your examples to the contrary.
I feel like a broken record but Enhancers! lncRNAs! siRNAs! Binding sites! Other gene regulatory regions! Epigenetic nucleosome modifications! Chromatin remodeler sites!
Oh, there’s your problem. A lot has changed. You refuse to see the sea change happening around you because it means you’re out of date.
I was happy to reply to you and engage pleasantly originally but you are only engaging with people that know less about biology than you do. You are not an expert if you last studied biology decades ago and can’t remember the details. You certainly aren’t enough of an authority on the subject to question a contemporary article published in Science or the work of other researchers currently in the field.
I really, really encourage you to read these papers thoroughly. You are the target audience-- people who learned the machine model of the cell and who are gripping it so tightly that they are blind to the nuance that we’ve uncovered. I also encourage you to not write insults about people who disagree with you, especially people with more domain knowledge than you have.
Every sperm isn’t sacred and every piece of DNA isn’t with purpose, otherwise explain ferns and plants having hundreds of times more DNA than higher functioning life forms.
deleted by creator