5 ms·

As far as the purpose of DNA is to tell the rest of the cell what proteins to synthesize, over 85% percent of our DNA is never translated to protein [1]. But le

by lake99 8y ago

As far as the purpose of DNA is to tell the rest of the cell what proteins to synthesize, over 85% percent of our DNA is never translated to protein [1]. But leave alone our knowledge of DNA, biology rarely works in a manner that's best suited for functional efficiency. For examples, look at how the vagus nerve evolved, or look at vestigial organs. The question for the gene is rarely "is this the most efficient way of doing things?" Rather, it is "is this strategy good enough for me (and my descendants) to pass on my genes?" [1] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3205562/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3205562/

stanfordkid 8y ago
That's a pretty cursory understanding of how DNA works. The "Junk DNA" hypothesis has long been invalidated. The non-coding genome is a large part of what causes us to look different from a mouse or a fruit-fly. Gene regulation (what gene to transcribe, and when) is largely controlled by non-coding DNA: https://en.wikipedia.org/wiki/Regulation_of_gene_expression https://en.wikipedia.org/wiki/Regulation_of_gene_expression There are energy costs associated with useless information being stored and transcribed in the genome... so it is pretty reasonable to believe that information theory does play some (however minor) role in how data is stored.
- mannykannot 8y ago
  We are drifting away from the original issue here. 'However minor' is a long way from near-maximal efficiency, and in the context of the original claim, 'efficient' means compact encoding. The fact that the DNA involved in gene regulation is mostly non-coding does not mean that most non-coding DNA has a regulatory purpose. If it did, changes in non-coding DNA would be more important, in aggregate, than changes in coding DNA are, with respect to evolution and disease, on account of its prevalence.
  - stanfordkid 8y ago
    Junk DNA is a phrase biologists use for describing the long held (and recently disproven) idea that non-coding DNA ("dna not coding for proteins") is unimportant relative to coding regions (genes). Most non-coding DNA does have a regulatory purpose. Things like copy number variations (where information is "duplicated") between promoters and enhancers can can change the rate at which particular genes get transcribed. This is my point: that viewing the genome as "information" in the simple sense of each ATCG nucleotide corresponding to bits is absurd. The genome is a geometric AND chemical entity and encodes information using both paradigms. My point is not to say that you are wrong, but rather that you do not know. It is FAR from well established that the genome is inefficient at storing information.
    - mannykannot 8y ago
      I don't know, you don't know, but only one of us is using speculative arguments (and, in at least one earlier case, fantasy, as lake99 pointed out above) to support her opinion. From an information-theoretic point of view (which is where we started) even if all non-coding DNA had some purpose, it would not be a sufficient basis for assuming that it is close to the most information-theoretically efficient implementation. On the other hand, the fact that whole genomes can be handily compressed, with straightforward Huffman encoding techniques, settles the infomation-theoretic efficiency question, regardless of whether your speculation about the usefulness of all non-coding DNA is correct.
- lake99 8y ago
  Neither I nor the paper I cited use the phrase "Junk DNA". > The non-coding genome is a large part of what causes us to look different from a mouse or a fruit-fly. Now that's just fantasy. There have been a lot of changes since our common ancestors with mice and fruit flies. We are all animals and obviously would share genes that perform analogous functions -- like common genes for controlling wing shapes and organ shapes. But would you like to point me to evidence in the human DNA that codes for fruit fly wings? And what role do you think having virus DNA in our genome plays in our development? DNA encodes information. Information theory does play a role. But as mannykannot pointed out, the topic of the conversation is something else.

by lake99 8y ago

stanfordkid 8y ago

That's a pretty cursory understanding of how DNA works. The "Junk DNA" hypothesis has long been invalidated. The non-coding genome is a large part of what causes us to look different from a mouse or a fruit-fly. Gene regulation (what gene to transcribe, and when) is largely controlled by non-coding DNA: https://en.wikipedia.org/wiki/Regulation_of_gene_expression https://en.wikipedia.org/wiki/Regulation_of_gene_expression There are energy costs associated with useless information being stored and transcribed in the genome... so it is pretty reasonable to believe that information theory does play some (however minor) role in how data is stored.

mannykannot 8y ago
We are drifting away from the original issue here. 'However minor' is a long way from near-maximal efficiency, and in the context of the original claim, 'efficient' means compact encoding. The fact that the DNA involved in gene regulation is mostly non-coding does not mean that most non-coding DNA has a regulatory purpose. If it did, changes in non-coding DNA would be more important, in aggregate, than changes in coding DNA are, with respect to evolution and disease, on account of its prevalence.
- stanfordkid 8y ago
  Junk DNA is a phrase biologists use for describing the long held (and recently disproven) idea that non-coding DNA ("dna not coding for proteins") is unimportant relative to coding regions (genes). Most non-coding DNA does have a regulatory purpose. Things like copy number variations (where information is "duplicated") between promoters and enhancers can can change the rate at which particular genes get transcribed. This is my point: that viewing the genome as "information" in the simple sense of each ATCG nucleotide corresponding to bits is absurd. The genome is a geometric AND chemical entity and encodes information using both paradigms. My point is not to say that you are wrong, but rather that you do not know. It is FAR from well established that the genome is inefficient at storing information.
  - mannykannot 8y ago
    I don't know, you don't know, but only one of us is using speculative arguments (and, in at least one earlier case, fantasy, as lake99 pointed out above) to support her opinion. From an information-theoretic point of view (which is where we started) even if all non-coding DNA had some purpose, it would not be a sufficient basis for assuming that it is close to the most information-theoretically efficient implementation. On the other hand, the fact that whole genomes can be handily compressed, with straightforward Huffman encoding techniques, settles the infomation-theoretic efficiency question, regardless of whether your speculation about the usefulness of all non-coding DNA is correct.
lake99 8y ago
Neither I nor the paper I cited use the phrase "Junk DNA". > The non-coding genome is a large part of what causes us to look different from a mouse or a fruit-fly. Now that's just fantasy. There have been a lot of changes since our common ancestors with mice and fruit flies. We are all animals and obviously would share genes that perform analogous functions -- like common genes for controlling wing shapes and organ shapes. But would you like to point me to evidence in the human DNA that codes for fruit fly wings? And what role do you think having virus DNA in our genome plays in our development? DNA encodes information. Information theory does play a role. But as mannykannot pointed out, the topic of the conversation is something else.