Thank you for taking the time to respond, I respect your knowledge and agree with you for the most part. From an evolutionary perspective there’s very little pressure to cull genetic material that does not have a purpose, genome replication is already taking place and takes very little overall energy/time.
There may not be as much useless DNA in the system as previously thought, but not every codon pair has a use. There are undoubtedly identical transcription codes being suppressed in one section of DNA that are active in other regions, and it may have been useful to have that extra region available if pressures ever applied that caused that region to be reactivated, but if mutation occurred and caused that region to no longer have the original blueprint it was coding for, it could theoretically create actual evolutionary pressure to eliminate/suppress that section of the genome, it could be suppressed/inactive harmful DNA, not junk but also not beneficial.
My biggest hang-up on the whole “every codon has a purpose” argument is that it blatantly ignores the evidence occurring so much more frequently at “lower” life forms. Eukaryotic single cell organisms swap DNA rather readily, it’s a much higher risk/reward mechanism of evolution, a lot of that DNA, if it turns out to be beneficial, will be ancillary to the actual genes with benefit. Plants have genomes that vary in length from generation up generation, often times much larger than required, maybe it’s because they chill in the sun all day and are more susceptible to genetic mutation, but just because there’s extra targets for codon swapping, doesn’t mean that DNA is set there with purpose. It just exists. It may have been beneficial at one point, but it’s only there because it isn’t detrimental enough to have selection pressure repercussions. If pressures were high enough they every codon mattered, (or if it were designed intelligently so that every codon mattered) a lot of genomes (I’m not to nervous to claim I believe all genomes) would be shorter due to junk culling, it’s just such a small factor in the schema that it isn’t ever selected against.
You feel that if a codon isn’t meant for something, if it doesn’t have a purpose– then it is junk. This is a mindset that is reflective of the machine model of the cell. We used to expect that each protein was bespoke for a function, each transcript necessary.
The whole paradigm shift at hand is this model falls flat, even for coding regions. I think you’re actually very spot in here with the prokaryotic DNA or the plant genomes (love me some violets for their weird genomes). Some parts of a genome will rapidly change and appear to serve no real purpose, but the next bite is the important one: even if it seems like there isn’t a purpose, like a top-down prescription for functionality, those regions are still doing something while they are present.
For example, some long non-coding regions affect the likelihood that a person will develop Parkinson’s disease, or in the case of plants with various polyploidies, the relative expression of their genes won’t necessarily change, but the absolute expression may.
Basically, you aren’t wrong that these regions dont have a purpose, because no genes have a purpose. The cell isn’t a machine.
Thank you for taking the time to respond, I respect your knowledge and agree with you for the most part. From an evolutionary perspective there’s very little pressure to cull genetic material that does not have a purpose, genome replication is already taking place and takes very little overall energy/time.
There may not be as much useless DNA in the system as previously thought, but not every codon pair has a use. There are undoubtedly identical transcription codes being suppressed in one section of DNA that are active in other regions, and it may have been useful to have that extra region available if pressures ever applied that caused that region to be reactivated, but if mutation occurred and caused that region to no longer have the original blueprint it was coding for, it could theoretically create actual evolutionary pressure to eliminate/suppress that section of the genome, it could be suppressed/inactive harmful DNA, not junk but also not beneficial.
My biggest hang-up on the whole “every codon has a purpose” argument is that it blatantly ignores the evidence occurring so much more frequently at “lower” life forms. Eukaryotic single cell organisms swap DNA rather readily, it’s a much higher risk/reward mechanism of evolution, a lot of that DNA, if it turns out to be beneficial, will be ancillary to the actual genes with benefit. Plants have genomes that vary in length from generation up generation, often times much larger than required, maybe it’s because they chill in the sun all day and are more susceptible to genetic mutation, but just because there’s extra targets for codon swapping, doesn’t mean that DNA is set there with purpose. It just exists. It may have been beneficial at one point, but it’s only there because it isn’t detrimental enough to have selection pressure repercussions. If pressures were high enough they every codon mattered, (or if it were designed intelligently so that every codon mattered) a lot of genomes (I’m not to nervous to claim I believe all genomes) would be shorter due to junk culling, it’s just such a small factor in the schema that it isn’t ever selected against.
I would encourage you to read the linked Science paper and Dan Nichol’s paper, Is the Cell Really a Machine?
You feel that if a codon isn’t meant for something, if it doesn’t have a purpose– then it is junk. This is a mindset that is reflective of the machine model of the cell. We used to expect that each protein was bespoke for a function, each transcript necessary.
The whole paradigm shift at hand is this model falls flat, even for coding regions. I think you’re actually very spot in here with the prokaryotic DNA or the plant genomes (love me some violets for their weird genomes). Some parts of a genome will rapidly change and appear to serve no real purpose, but the next bite is the important one: even if it seems like there isn’t a purpose, like a top-down prescription for functionality, those regions are still doing something while they are present.
For example, some long non-coding regions affect the likelihood that a person will develop Parkinson’s disease, or in the case of plants with various polyploidies, the relative expression of their genes won’t necessarily change, but the absolute expression may.
Basically, you aren’t wrong that these regions dont have a purpose, because no genes have a purpose. The cell isn’t a machine.
Three cheers for Dan Nichol’s paper.
Here’s a direct link to the PDF found on Philpapers.org.