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Science

DNA 'Knockouts' Reveal Genes Humans Don't Need (sciencemag.org) 93

sciencehabit writes: Although humans have about 20,000 genes, exactly what most of them do inside our body's cells is still murky. One way to learn more is to find people who lack a working copy of a particular gene and see how that affects their health. Such so-called knockouts are scarce in the general population. But a new study points to a more efficient way to find them: Search the DNA of people from a culture in which marrying a relative is common. The study has found a number of genes that we seemingly can do without, including those thought to prevent serious diseases. And one healthy mother completely lacked a gene called PRDM9 that is involved in shuffling chromosomes during the formation of eggs and sperm. Mice lacking the gene are sterile.
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DNA 'Knockouts' Reveal Genes Humans Don't Need

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  • by sinij ( 911942 ) on Friday March 04, 2016 @01:57PM (#51637819)
    Our genome is spaghetti code of the worst kind. If God exists, he is horrible coder.
    • Horrible from a human perspective. He is transcendent, we are just too dumb to understand the inner beauty.

    • Re:Sphagetti code (Score:5, Interesting)

      by Wycliffe ( 116160 ) on Friday March 04, 2016 @02:15PM (#51637981) Homepage

      Our genome is spaghetti code of the worst kind. If God exists, he is horrible coder.

      Looking at the genome (or our brain) to understand how it works is kindof like looking at the end result of a neural net or genetic algorithm. The millions of random mutations get the right result based on the selection criteria (in this case survival). The animal world has plenty of extreme macroscopic examples of this whether it is extremely painful reproduction, deadly reproduction, insane impractical appendages, it doesn't really matter as long as your generation "wins". Some AI scientists have tried to reverse engineer relatively simple code generated by genetic algorithms and have found stuff that as far as they can tell shouldn't even work but exploits some small loophole in either the code, the hardware, or the selection criteria. When I was in HS, I did some GA stuff that failed miserably at midnight because the bots were taking advantage of minor variations in the random number generator and those assumptions failed as soon as the day changed. Our genome is this times a million. The number of flukes, switchbacks, random hacks, and things that shouldn't work but manage to because of some other random mutation is probably mind-boggling.

    • by zx75 ( 304335 )

      Are you kidding? Considering that god wrote a program that is self-modifying, evolutionary, infinitely adaptable, and capable of self-reflection and consciousness from a few basic parameters that started the size of an infinitesimal speck containing all the energy in the universe... I would say god is an uncomprehendingly amazing coder!

    • Re:Sphagetti code (Score:4, Insightful)

      by Zeio ( 325157 ) on Friday March 04, 2016 @02:35PM (#51638215)

      NO.

      Its called epigenetics and three dimension conformation and methylation groups.

      Gene expression relies on both methylation, epigenetics (inheritable - this is big as experience and environment can create gene expression changes that are passed to offspring) and three dimensional configuration of "useless genes" have an effect on gene expression.

      Your notion of double helix and guanine tyrosine adensosine cytosine and uracil for thymine in RNA being simple "code" is absurd, disproved and ridiculous.

      Removal of ""useless"" codons WILL change gene expression and cause huge problems which are not able to be predicted.

      I noticed that most of the domain specific jargon words I'm using aren't showing up as known in Chrome so the world is not, according to the bulk data spell correction, even thinking about this issue of methylation, epigenetics and DNA codons and gene expression correctly.

      • Removal of ""useless"" codons WILL change gene expression and cause huge problems which are not able to be predicted.

        Yet.

        At some point we will be able to not only predict what genes will do, we will be able to optimize our genetic code and harden it.

        • by Zeio ( 325157 )

          Mapping this out will take a lot of time. You'll need a "life simulator" to see what every codon does. Also you would need an even more immense "life simulator" to take into account what all the side effects of the various methylation groups are. Sure, its possible to figure this out, but the article is not good at all - indicating there is a lot of "junk" in the genome is useless. Indicating certain sequences are knockouts and important is hardly a new concept. Now find the gene that causes autism if its t

        • by vivian ( 156520 )

          We probably could eventually optimise our genetic code for our current conditions and environment - however there is probably a lot of 'unused' code that then gets turned on when envronmental conditions change or different stresses are introduced, making it possible for us as a species to rapidly evolve into something more able to survive, so removing al that 'useless' code would most likely turn out to be a big mistake when we one day discover that actually a lot of those unused genes would have been reall

      • by HiThere ( 15173 )

        While there's some truth in what you say, there's not much. Epigenetics are rather like state variables, Methylation is analogous to a read-protect and de-methylation to the removal of such protections. Most epigenetic markers are removed between generations, but some slip through, an don't know the reasons. (That's not my area of expertise, but I believe that nobody currently knows why.)

        OTOH, "unused" genes may be needed as spacers, as some enzymes depend on a particular separation between the pieces t

        • Removal of SOME "useless" codons will change gene expression. Removal of other "useless" codons will have no effect.

          But we don't have a very good clue of which is which, either, and what won't affect one individual if you made a tweak might affect another with differences someplace else, right?

          To say that the chromosomes are just strings of nucleotides would, indeed, be foolish. This doesn't mean that code isn't a good, even an excellent, analogy.

          Code would be a good analogy if there were something in the system that's like a CPU.

          • by HiThere ( 15173 )

            Well, you could nominate the ribosome as a multi-processor CPU, but the analogy is really too loose to carry that far.

            You don't use an analogy to get a detailed understanding of something, only to get a rough idea. For detailed understanding you need to study the thing itself. Like this study.

    • Re: (Score:3, Funny)

      by Tablizer ( 95088 )

      Our genome is spaghetti code of the worst kind. If God exists, he is horrible coder.

      It's been obfuscated for security. He/she doesn't want humans mucking with it.

      • Our genome is spaghetti code of the worst kind. If God exists, he is horrible coder.

        It's been obfuscated for security. He/she doesn't want humans mucking with it.

        Maybe being a master coder and tinkerer, the code base is a mixture of intended functionality, experiments, 'what if's, 'just in case' and 'just because'. It works well enough, as intended and it is fun just seeing things play out. God may not be playing dice, but may still be happy just sitting back and observing how things turn out.

        • by Tablizer ( 95088 )

          mixture of intended functionality, experiments, 'what if's, 'just in case' and 'just because'

          "Let's see what happens if I send in this odd Trump critter..."

    • We only use 50% of our brain ... oh, now we know we use a vast amount more than that.

      What I am trying to get at, is while something appears to be unused, their use may be a lot more subtle that we suspect. For example it can kick in as protective mechanism in some context, but otherwise appear dormant or non-functional. From a coding context, this is like the function that is called in 2% of cases, every 2 years, but not having it could mean a system crash of the worst kind. Again from a coding context, thi

  • "Search the DNA of people from a culture in which marrying a relative is common."

    So they went to the Appalachians to do the study?

  • by peter303 ( 12292 ) on Friday March 04, 2016 @02:00PM (#51637849)
    I heard there are between 10 and 20 thousand human genomes fully sequenced now. Both Craig Venter and Obama are trying to jack that up to a million. Then Analytics will replace a lot of painstaking lab work. (but not all)
  • Studies reveal that humans are also able to survive without a functioning X-Gene.
  • Then again (Score:5, Insightful)

    by choke ( 6831 ) on Friday March 04, 2016 @02:18PM (#51638007) Homepage

    You can remove half the parts of my diesel engine. It'll work .. until the set of conditions that the specific part is intended to address occur at which time it will fail. Sometimes dramatically.

    The human system is significantly more complex than my diesel engine, and the set of conditions that it encounters are significantly more complex as well.

    The thought that ignorance of fact is evidence of fact is appalling. That we don't know what a part does, in no way indicates anything other than our own lack of understanding.

    • by Hylandr ( 813770 )

      +1

      Hell, +10k.

      So much this.

    • Based just on the title, I was already agreeing, thinking that is the most arrogant yet stupid headline I've ever seen. And I guess now we can start creating designer babies by removing all this junk, until the human race needs to cope with something those genes provided.

  • Should be the "beneficiaries" of such a breakthrough.

    Mind you, it all probably means that once more there's a publicly noticeable epic fail. Remember of course that a lot of those science think that around 90% of DNA is just junk.

  • Plot twist (Score:5, Funny)

    by wardrich86 ( 4092007 ) on Friday March 04, 2016 @02:20PM (#51638029)
    Plot twist: The genomes they lack are the ones that keep the rest of us from wanting to marry our siblings and cousins. Could this be the beginning of the end?
    • by Anonymous Coward

      They are talking about muslims.

  • by ThatsNotPudding ( 1045640 ) on Friday March 04, 2016 @02:30PM (#51638149)
    What one fool would call 'junk DNA', the ox-slow grinding of disease and toxins would call a chance for a few members of the species to survive a near-extinction event.
  • " Search the DNA of people from a culture in which marrying a relative is common"

    Kansas?

    • " Search the DNA of people from a culture in which marrying a relative is common"
      Kansas?

      No, they said culture

  • by Gravis Zero ( 934156 ) on Friday March 04, 2016 @02:36PM (#51638223)

    there is a lot of DNA that encodes for stuff we don't need... until we do. you could remove lots of genes that are only active under certain conditions if you can be sure you will never meet those conditions. however, the optimal evolutionary pattern is to hedge your bets.

    • Exactly. Just like you don't need a seat belt to drive a car.
      The parameter space that can be easily probed is too small to say for certain that a gene is not needed.

    • by HiThere ( 15173 )

      You are assuming that it *IS* useful. That's the conservative assumption, and for any particular gene it may be true. But many have never been useful, and are just random mutations that happened to be carried along. See "Neutral Drift". Others are actively harmful, but not harmful enough to have been selected out ... yet. Others were at one point useful, and would still be useful if the original occasion reoccurred. Others were once useful, but have since mutated into forms that are just useless...or

  • by kheldan ( 1460303 ) on Friday March 04, 2016 @02:42PM (#51638279) Journal
    I'm under the impression that much (if not all) of the so-called 'junk DNA' that seemingly does nothing, is more like 'error handling' or 'conditional' code that rarely, if ever, gets activated -- but that might save our lives. For instance, a recent Slashdot story: Viral 'Fossils' In Our DNA May Help Us Fight Infection [slashdot.org]
  • by ooloorie ( 4394035 ) on Friday March 04, 2016 @02:47PM (#51638329)
    Most of our genes don't do much of anything most of the time. But that's true of many things in our environment. Car analogy? I can sabotage your headlights, your seat belts, your rear seats, your locks, your airbags, your dome lights, your climate control, your emission filters and catalytic converter and... you might not even notice until months later. That doesn't mean that those items don't have any function.

    In fact, large numbers of genes probably exist only to be used when you are sick or environmentally stressed. Many other genes give you redundant functionality, or functionality that individually only increases your performance on some task a little bit. Many genes have significant effects only in the brain, where it is very hard to find differences.

    Don't get me wrong: the information that some gene can be deleted without being lethal is useful information. But it doesn't mean that you "don't need them".

  • God, you boomers are so out of it. miRNA, circRNA, sRNA, mRNA all show that our genome uses environmental triggers to shift express different proteins to adapt to different environmental conditions. You've even got tertiary metabolic pathways that express when you suppress the first two pathways with medications.

    Look, it's not noise DNA. It's there for a reason. You just aren't in the environmental conditions needed to cause it to express itself.

  • People messing with their genes are gonna turn out more messed up. Dont mess with recent scientific studies

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