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The article above has nothing to do with Junk DNA. "All genes" is still about 1.5% of the genome. I think Junk DNA is a bad term for the parts of the genome th

by dkural 8y ago

The article above has nothing to do with Junk DNA. "All genes" is still about 1.5% of the genome. I think Junk DNA is a bad term for the parts of the genome that describe it. In human-engineered physical systems, we are used to all or most of the parts having a purpose of some kind, even if it is an aesthetic purpose. The genome is more like source code that evolved over millions of commits, and has code from way back when, for different use cases. It also has "injected code" ie ancient viral DNA, and other weird artifacts that's not relevant to the functioning code base of today. Sure, it is useful from a meta-evolutionary perspective, those parts can be refashioned for another use... but so can real-world "junk" :)

resource0x 8y ago
Quote: Male mice grow ovaries instead of testes if they are missing a small region of DNA that doesn't contain any genes, finds a new paper published in Science. Source: https://www.crick.ac.uk/news/science-news/2018/06/14/non-coding-dna-changes-the-genitals-youre-born-with/ https://www.crick.ac.uk/news/science-news/2018/06/14/non-cod... EDIT: I think the finding is significant enough to warrant a separate discussion. Submitted a link: https://news.ycombinator.com/item?id=17361545 https://news.ycombinator.com/item?id=17361545
- dkural 8y ago
  The press release is misleading - no one is claiming 98% of the DNA is "junk", contrary to what the press release claims with no evidence. Regulatory regions around genes are understood be crucial to gene function and taught in undergraduate education. Usually people claim that mobile elements + repetitive regions constitute the "junk" region, which is about 40% of the genome. Also, there are dozens of studies showing you can survive with large chunks of it missing. Each human in fact has thousands of such structural variations.
  - resource0x 8y ago
    Not sure what you mean. Dawkins in 2009: “Leaving pseudogenes aside, it is a remarkable fact that the greater part (95 percent in the case of humans) of the genome might as well not be there, for all the difference it makes.” The quote is all over the internet. E.g., see http://egnorance.blogspot.com/2013/02/richard-dawkins-on-junk-dna-in-2009.html http://egnorance.blogspot.com/2013/02/richard-dawkins-on-jun...
    - dkural 8y ago
      Huh! I've learned something. Honestly, I have a PhD, doing human genomics, and to me Dawkins is a popular science writer. I don't know anyone in the field of genomics who is an actual working scientist who believes in the 95% number. Note that the Encode Project defines functional as being transcribed, which is not a widely accepted definition of functional. The whole idea of "function" itself brings a lot of subjective notions into play. As I said in the parent, I also think "junk dna" is a terrible term. What I prefer stating is, in agreement with Ohno/Kimura's theory of neutral selection, the vast majority of our genome is not under positive or negative selection - i.e. mutations occurring there are neither detrimental, nor helpful, for fitness. If you look at allele ratios of variants across the genome, the vast majority show evidence of neutral drift.
      - resource0x 8y ago
        For fairness sake, quote from the same post (Dawkins changed his mind by 2012): "So you can think of the protein-coding genes as being sort of the toolbox of subroutines which is pretty much common to all mammals -- mice and men have the same number, roughly speaking, of protein-coding genes and that's always been a bit of a blow to self-esteem of humanity. But the point is that that was just the subroutines that are called into being; the program that's calling them into action is the rest [of the genome] which had previously been written off as junk." This makes sense to me (as a programmer :). But I wonder if someone managed to figure out the language in which the "caller" code is written. How does it say: call subroutine at position X, then if (condition), call subroutine at position Y, etc... I was not able to find any info on this.
ravinizme 8y ago
The coding part of the genes are 1.5% of the genomes.it is called the Exome.(32 millions) But when looking at all genes (including UTR, pseudogenes) from a basepair prespective It's closer to 40% of the genome.(1.2 billion bases)

by dkural 8y ago

resource0x 8y ago

Quote: Male mice grow ovaries instead of testes if they are missing a small region of DNA that doesn't contain any genes, finds a new paper published in Science. Source: https://www.crick.ac.uk/news/science-news/2018/06/14/non-coding-dna-changes-the-genitals-youre-born-with/ https://www.crick.ac.uk/news/science-news/2018/06/14/non-cod... EDIT: I think the finding is significant enough to warrant a separate discussion. Submitted a link: https://news.ycombinator.com/item?id=17361545 https://news.ycombinator.com/item?id=17361545

dkural 8y ago
The press release is misleading - no one is claiming 98% of the DNA is "junk", contrary to what the press release claims with no evidence. Regulatory regions around genes are understood be crucial to gene function and taught in undergraduate education. Usually people claim that mobile elements + repetitive regions constitute the "junk" region, which is about 40% of the genome. Also, there are dozens of studies showing you can survive with large chunks of it missing. Each human in fact has thousands of such structural variations.
- resource0x 8y ago
  Not sure what you mean. Dawkins in 2009: “Leaving pseudogenes aside, it is a remarkable fact that the greater part (95 percent in the case of humans) of the genome might as well not be there, for all the difference it makes.” The quote is all over the internet. E.g., see http://egnorance.blogspot.com/2013/02/richard-dawkins-on-junk-dna-in-2009.html http://egnorance.blogspot.com/2013/02/richard-dawkins-on-jun...
  - dkural 8y ago
    Huh! I've learned something. Honestly, I have a PhD, doing human genomics, and to me Dawkins is a popular science writer. I don't know anyone in the field of genomics who is an actual working scientist who believes in the 95% number. Note that the Encode Project defines functional as being transcribed, which is not a widely accepted definition of functional. The whole idea of "function" itself brings a lot of subjective notions into play. As I said in the parent, I also think "junk dna" is a terrible term. What I prefer stating is, in agreement with Ohno/Kimura's theory of neutral selection, the vast majority of our genome is not under positive or negative selection - i.e. mutations occurring there are neither detrimental, nor helpful, for fitness. If you look at allele ratios of variants across the genome, the vast majority show evidence of neutral drift.
    - resource0x 8y ago
      For fairness sake, quote from the same post (Dawkins changed his mind by 2012): "So you can think of the protein-coding genes as being sort of the toolbox of subroutines which is pretty much common to all mammals -- mice and men have the same number, roughly speaking, of protein-coding genes and that's always been a bit of a blow to self-esteem of humanity. But the point is that that was just the subroutines that are called into being; the program that's calling them into action is the rest [of the genome] which had previously been written off as junk." This makes sense to me (as a programmer :). But I wonder if someone managed to figure out the language in which the "caller" code is written. How does it say: call subroutine at position X, then if (condition), call subroutine at position Y, etc... I was not able to find any info on this.

ravinizme 8y ago

The coding part of the genes are 1.5% of the genomes.it is called the Exome.(32 millions) But when looking at all genes (including UTR, pseudogenes) from a basepair prespective It's closer to 40% of the genome.(1.2 billion bases)