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This is a widely held misconception. Mammalian genomes contain about 50% of their DNA as repeated sequences, and although there are people who can imagine uses

This is a widely held misconception. Mammalian genomes contain about 50% of their DNA as repeated sequences, and although there are people who can imagine uses for those sequences, there is no evidence that they are required or even evolutionarily advantageous. The idea that modern higher organisms have been "optimized" so that every part is essential is not well supported by evidence, and there are many examples of features that simply are historical artifacts or "not-sufficiently harmful". Many evolutionary biologists are comfortable with neutral theories consistent with the idea that large portions of the genome are not under strong (or perhaps even moderate) selection.

gwright 5y ago
biological version of dead code with no time allocated in the roadmap for cleanup and refactoring?
- frenchyatwork 5y ago
  Only vaguely. If the DNA was to be compared with our programming languages, it would be like INTERCAL, but a million times worse. Sections of the genome interact not only with the code right around them, but also with code far away, as a result of the chromosomal folding. So a section of 100 nucleotides might not do anything if you splice it out and throw various enzymes and other chemicals at it, and it might not even matter that much which nucleotides they are, but if you remove them and change the shape of the chromosome, it might not work the same way. A lot of our knowledge of genetic is limited to the things that are easy to test.
- UnFleshedOne 5y ago
  Except our machines are designed around the idea of isolating components and minimizing unintended side effects, while biology has no such compulsion. Imagine if an extra semicolon in one of your unused files shifted electrical distribution on storage media and that had all kinds of downstream effects on unrelated systems and those effects were critical for multiple other functions. Only increase complexity enough so the whole contraption is NOT brittle.
pbh101 5y ago
You’re talking about messiness in the genotype, but selection pressure happens to the phenotype. The latter I think controls more of what ends up in the former. Which is what we see all the time in programming: software wins because of its effect, not usually the lines of code needed (or not) to get there.
- fastaguy88 5y ago
  I'm not sure I understand your argument, but if large portions of the genome have no effect on phenotype, then perhaps we can both agree that those regions would not be under selection. Pressure on the phenotype cannot directly alter the genotype (no Lamarkism), but it could select for or against the fraction of the population with a particular genotype. But only if the genotype produces a phenotype.
  - cma 5y ago
    Wouldn't assuming a one-copy rule end state is natural cause immense issues with recessive genetic disorders (which could in turn select against it), and also make chromosomal-crossover produce sterilized but viable young at a much higher rate?
echelon 5y ago
> This is a widely held misconception. Mammalian genomes contain about 50% of their DNA as repeated sequences, and although there are people who can imagine uses for those sequences, there is no evidence that they are required or even evolutionarily advantageous. If you remove noncoding "junk DNA", you alter the higher level spatial configuration of DNA. Histone winding changes which promoter regions are accessible, gene dosing is altered, binding affinity and kinetics change, etc. These are dynamical equations you're dramatically altering. Non-coding DNA also likely shields against several classes of random point mutations, base substitutions, transposition, etc. preventing cancer and cell physiological disease states. It's also important for maintaining alignment during crossover. If it truly served no purpose, it would be gone. > The idea that modern higher organisms have been "optimized" so that every part is essential Essential is the wrong word here. Relying on every part for survival would put us at risk. We have plenty of built in redundancies to support degradation, failure, and loss of multiple systems and functions. I get your argument, but I still disagree. At the species / population level, we have been optimized as wholesale organisms as best as development and body plans will allow. Everything not subject to pressure will get washed away. Despite our vestigial tails, the coccyx supports our weight while we are seated. As I postulated before, the appendix probably has a net positive function in supporting gut microflora and our "junk DNA" plays a role at the molecular level.
- Dylan16807 5y ago
  > If it truly served no purpose, it would be gone. Why? Removing it serves no purpose either.
- fastaguy88 5y ago
  The statement that at some level species have been optimized is a religious belief, not a scientific one. Species are at the end of an evolutionary history that ended in the present. There is no reason to believe that that endpoint is optimal in any sense. It is certainly not globally optimal, and absent very strong selection, it may not even be locally optimal. Evolution explores an infinitesimal fraction of the possible states/pathways available. Without more thorough exploration and strong selection, there is no reason to believe things are optimal. I think I’m not going out on a limb to say that no modern evolutionary biologist believes organisms are optimal. They simply survived.

gwright 5y ago

biological version of dead code with no time allocated in the roadmap for cleanup and refactoring?

frenchyatwork 5y ago
Only vaguely. If the DNA was to be compared with our programming languages, it would be like INTERCAL, but a million times worse. Sections of the genome interact not only with the code right around them, but also with code far away, as a result of the chromosomal folding. So a section of 100 nucleotides might not do anything if you splice it out and throw various enzymes and other chemicals at it, and it might not even matter that much which nucleotides they are, but if you remove them and change the shape of the chromosome, it might not work the same way. A lot of our knowledge of genetic is limited to the things that are easy to test.
UnFleshedOne 5y ago
Except our machines are designed around the idea of isolating components and minimizing unintended side effects, while biology has no such compulsion. Imagine if an extra semicolon in one of your unused files shifted electrical distribution on storage media and that had all kinds of downstream effects on unrelated systems and those effects were critical for multiple other functions. Only increase complexity enough so the whole contraption is NOT brittle.

pbh101 5y ago

You’re talking about messiness in the genotype, but selection pressure happens to the phenotype. The latter I think controls more of what ends up in the former. Which is what we see all the time in programming: software wins because of its effect, not usually the lines of code needed (or not) to get there.

fastaguy88 5y ago
I'm not sure I understand your argument, but if large portions of the genome have no effect on phenotype, then perhaps we can both agree that those regions would not be under selection. Pressure on the phenotype cannot directly alter the genotype (no Lamarkism), but it could select for or against the fraction of the population with a particular genotype. But only if the genotype produces a phenotype.
- cma 5y ago
  Wouldn't assuming a one-copy rule end state is natural cause immense issues with recessive genetic disorders (which could in turn select against it), and also make chromosomal-crossover produce sterilized but viable young at a much higher rate?

echelon 5y ago

> This is a widely held misconception. Mammalian genomes contain about 50% of their DNA as repeated sequences, and although there are people who can imagine uses for those sequences, there is no evidence that they are required or even evolutionarily advantageous. If you remove noncoding "junk DNA", you alter the higher level spatial configuration of DNA. Histone winding changes which promoter regions are accessible, gene dosing is altered, binding affinity and kinetics change, etc. These are dynamical equations you're dramatically altering. Non-coding DNA also likely shields against several classes of random point mutations, base substitutions, transposition, etc. preventing cancer and cell physiological disease states. It's also important for maintaining alignment during crossover. If it truly served no purpose, it would be gone. > The idea that modern higher organisms have been "optimized" so that every part is essential Essential is the wrong word here. Relying on every part for survival would put us at risk. We have plenty of built in redundancies to support degradation, failure, and loss of multiple systems and functions. I get your argument, but I still disagree. At the species / population level, we have been optimized as wholesale organisms as best as development and body plans will allow. Everything not subject to pressure will get washed away. Despite our vestigial tails, the coccyx supports our weight while we are seated. As I postulated before, the appendix probably has a net positive function in supporting gut microflora and our "junk DNA" plays a role at the molecular level.

Dylan16807 5y ago
> If it truly served no purpose, it would be gone. Why? Removing it serves no purpose either.
fastaguy88 5y ago
The statement that at some level species have been optimized is a religious belief, not a scientific one. Species are at the end of an evolutionary history that ended in the present. There is no reason to believe that that endpoint is optimal in any sense. It is certainly not globally optimal, and absent very strong selection, it may not even be locally optimal. Evolution explores an infinitesimal fraction of the possible states/pathways available. Without more thorough exploration and strong selection, there is no reason to believe things are optimal. I think I’m not going out on a limb to say that no modern evolutionary biologist believes organisms are optimal. They simply survived.