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The Gene Is Having an Identity Crisis 257

Posted by kdawson
from the more-complicated-than-you-thought dept.
gollum123 writes "New large-scale studies of DNA are causing a rethinking of the very nature of genes. A typical gene is no longer conceived of as a single chunk of DNA encoding a single protein. It turns out, for example, that several different proteins may be produced from a single stretch of DNA. Most of the molecules produced from DNA may not even be proteins, but rather RNA. The familiar double helix of DNA no longer has a monopoly on heredity: other molecules clinging to DNA can produce striking differences between two organisms with the same genes — and those molecules can be inherited along with DNA. Scientists have been working on exploring the 98% of the genome not identified as the protein-coding region. One of the biggest of these projects is an effort called the Encyclopedia of DNA Elements, or 'Encode.' And its analysis of only 1% of the genome reveals the genome to be full of genes that are deeply weird, at least by the traditional standard of what a gene is supposed to be and do. The Encode team estimates that the average protein-coding region produces 5.7 different transcripts. Different kinds of cells appear to produce different transcripts from the same gene. And it gets even weirder. Our DNA is studded with millions of proteins and other molecules, which determine which genes can produce transcripts and which cannot. New cells inherit those molecules along with DNA. In other words, heredity can flow through a second channel."
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The Gene Is Having an Identity Crisis

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  • Memory RNA (Score:3, Interesting)

    by CRCulver (715279) <crculver@christopherculver.com> on Tuesday November 11, 2008 @07:11PM (#25727313) Homepage
    A thread on DNA and its relationship to RNA gives me a chance to ask: what ever happened to the idea that memory was encoded in RNA? In 1970s science fiction novels like Niven's A World out ot Time [amazon.com] , you had people learning new skills through the injection of RNA. When did it become clear that RNA had nothing to do with memory?
    • Re:Memory RNA (Score:5, Informative)

      by Ethanol-fueled (1125189) * on Tuesday November 11, 2008 @07:19PM (#25727393) Homepage Journal
      The answer lies in the RTFW (Read The F'in Wikipedia) article about Memory RNA [wikipedia.org]:

      One experiment that was purported to show a chemical basis for memory involved training planaria to solve an extremely simple "maze", then grinding them up and feeding them to untrained planaria to see if they would be able to learn more quickly. The experiment seemed to show such an effect, but it was later determined that the original planaria had left chemical tracks inside the maze itself that were not properly cleaned away before the next set of planaria were run.

      It's not a complete explanation, but it implies that pathfinding behavior(e.g. getting out of a maze) had much more to do with following a chemical "bread crumb" trail than using memory alone.

      • Re: (Score:2, Interesting)

        by postbigbang (761081)

        More interesting still was his machine that took cell detritus and 'instant elsewhere'd' it to an adjoining chamber. The idea being to flush the junk from cells and cause a fountain of rejuvenation. FTA, it might be one day feasible to ride a cell of bad or junk RNA.

      • Re: (Score:2, Interesting)

        by popmaker (570147)
        In other words: "No conclusion"? It HASN'T been ruled out? The way I understand it is that a large part of evolutionary theory ASSUMES that memory can't be inherited.
      • Re: (Score:3, Informative)

        by Fumus (1258966)

        One experiment that was purported to show a chemical basis for memory involved training planaria to solve an extremely simple "maze", then grinding them up and feeding them to untrained planaria to see if they would be able to learn more quickly.

        This reminds me of VG Cats [vgcats.com].
        So wrong..

    • Re:Memory RNA (Score:4, Interesting)

      by thepotoo (829391) <[thepotoospam] [at] [yahoo.com]> on Tuesday November 11, 2008 @07:20PM (#25727401)
      Well, I've not learned about RNA holding memory in any of my classes, and even Wikipedia has little to say [wikipedia.org] on the subject.

      I'd venture a guess that it's not correct (simply not enough evidence supporting it, but that has not yet been ruled out either [nih.gov].

      The bottom line is that we do not yet fully understand memory, in much the same way that we do not fully understand synapse formation in the brain. We should just wait and see before jumping to any conclusions (and maybe write a grant proposal or two along the way).

    • by SlashThat (859697)
      Well, it might sound like a cool idea, but this just wouldn't work. This kind of "memory" would be to slow to be useful, since it would involve long biological processes to decode the RNA (or DNA). It would be like storing a program's memory page on an external floppy disk.
      • by Ollabelle (980205)
        Perhaps, but maybe that's where innate fear of certain predators originates.
        • Re:Memory RNA (Score:4, Interesting)

          by shawb (16347) on Tuesday November 11, 2008 @10:14PM (#25728929)
          I think what you are referring to is more closely related to instinct than memory. Instinct is related to sets of behaviors that are performed naturally, learned. These are to some extent controlled by genes, but can be overridden by learning. I.E. genes will encode for certain basic neural pathways to be formed, but the brain's development will then be left to augment or diminish that pathway's strength.

          Memory is an entirely different system, in which patterns simulating previous stimuli are stored and available to be replayed or compared against. Calling the effect of instinct "ancestral memory" or "genetic memory" is at best a poetic interpretation, at worst a logical flaw similar to Lamarkian Evolution [wikipedia.org] wherein giraffes have long necks because their ancestors stretched out trying to graze from tall shrubs, then trees, rather than the Darwinian idea that giraffes have long necks because short necked giraffes did not live to reproduce as well as long necked ones.
    • Re: (Score:3, Insightful)

      by Atmchicago (555403)

      A very simple answer is that RNA degrades *extremely* rapidly. Injecting RNA could feasibly give a short change in phenotype, but it is hard to imagine that RNA would be able to encode something as long-lasting as memory.

    • Re:Memory RNA (Score:5, Informative)

      by joe_bruin (266648) on Tuesday November 11, 2008 @07:45PM (#25727661) Homepage Journal

      RNA is a copy of DNA created by an enzyme called RNA Polymerase [wikipedia.org]. All RNA Polymerase does is a simple copy. There is no mechanism for creating "new" RNA that contains data that is not already present in your genes. That is, your body does not contain any device that can write memory information to RNA strands.

      • by CODiNE (27417)

        Any new findings on instinct?

        • Re: (Score:3, Insightful)

          by 2nd Post! (213333)

          Can you define instinct so we can talk intelligently about it?

          • Re: (Score:3, Interesting)

            by lgw (121541)

            Stimulus-response patterns that are inherited, not learned. Some might exclude mere reflexes (patterns where the stimulus creates the response before/without brain activity) but I'm not sure that modifies the definition in a helpful way.

            It's really an interesting question. Seeming complex behavior patterns are clearly not learned, but present in each generation - where do they come from? This would seem to be software, not hardware, but where and how it it stored/passed on?

      • Re: (Score:2, Insightful)

        by rnaiguy (1304181)
        Sorry, not true. There ARE mechanisms for creating new RNA not encoded in the DNA. Enzymes can shuffle around RNA sequence (as in RNA splicing), or change single nucleotides. Interestingly, the base changes occur most often in the nervous system of mammals. However, as mentioned, RNA doesn't stick around long enough to be responsible for memory. http://en.wikipedia.org/wiki/Rna_editing [wikipedia.org]
  • by StefanJ (88986) on Tuesday November 11, 2008 @07:11PM (#25727317) Homepage Journal

    . . . A Human Genome Interpreter Project.

  • I Knew It (Score:5, Funny)

    by Nyall (646782) on Tuesday November 11, 2008 @07:15PM (#25727357) Homepage

    Not only does God code in machine language, but it is all spaghetti. Thats probably why eventually malfunction and die.

    • by Pichu0102 (916292) <pichu0102@gmail.com> on Tuesday November 11, 2008 @07:26PM (#25727457) Homepage Journal

      Thats probably why eventually malfunction and die.

      Some faster than others, apparently.

    • by Yvan256 (722131) on Tuesday November 11, 2008 @07:29PM (#25727495) Homepage Journal

      You have it backwards. God doesn't code in spaghetti machine language. The FSM itself coded God.

    • by Repton (60818) on Tuesday November 11, 2008 @08:41PM (#25728219) Homepage

      Well, what do you expect when you knock off a major project in under a week?

    • Re: (Score:3, Funny)

      by servognome (738846)
      Death is a feature... please consult your owners manual or contact customer service for more information - God
    • by jamesh (87723)

      I bet that obscure comments in God's code would put Larry Wall to shame too :) /* FIXME: Is free will a good idea? Review after beta testing... */

  • by repapetilto (1219852) on Tuesday November 11, 2008 @07:21PM (#25727405)
    Epigenetics [wikipedia.org]
    RNA Splincing [wikipedia.org]
    siRNA [wikipedia.org]
    • OK, well now that I actually read the article its a pretty good one. Anyway heres what is new (at least to me): "the Encode scientists estimate that a staggering 93 percent of the genome produces RNA transcripts"
      • Nevermind they were just talking about transcription factor binding sites. None of this is new stuff.
    • Second that, nothing is news in this report. Common knowledge on genetics is portrayed as fresh from the press. Probably every medium-size gene-annotation research facility, small or medium, has their private version of a gene database.

      Mod Parent Up
  • ...we had been assuming that the layout of cupholders determines what the make/model is?
    Somebody help me out here, I'm on pain meds and not thinking at 100% capacity...
    • by reverseengineer (580922) on Tuesday November 11, 2008 @08:33PM (#25728101)

      Think of it this way- if your protein-coding genes are the blueprints for a car, then epigenetics are the blueprints, operating procedures, and logistics for a mass production automobile factory. By reading your genes, you can find out the kinds of proteins that make you up. Similarly, car blueprints tell you how to make a car. A car, just one car. However, your cells are not putting out handbuilt cars. It's a modern Toyota factory going on in there, with continuous production and assembly. It's a marvel of mass production, with transcription, splicing, translation, post-translational modification, and relocation to the site of use all going on in multiple sites constantly. Production has to be carefully coordinated to make sure you have the right amounts of the right proteins delivered at the right times.

      Epigenetics is the guy at the factory who knows how many cars to build this month, and the guy who makes sure that 10,000 cars have 10,000 steering wheels available to put in. Epigenetics is the guy who tells the line to hold up on building doors, because there's a surplus of doors in the warehouse already and we should use those first. Epigenetics is not the stuff you are made of, but rather a system of production control of that stuff.

  • And do the midichlorians also carry the force?

    Seriously, though, I thought we already had mitochondria living in our cells that were also inherited...
    • by Bryansix (761547)
      In Episode V Yoda said the force is everywhere. In the trees, in the rocks, between the earth and the X-Wing. How do midichlorians even come remotely close to explaining any of that?
      • Perhaps they infect everything.
      • As much as I was unpleasantly gobsmacked by the Midichlorians thing, I do recognize it as an earnest attempt on Lucas' part to match up his universe with the real one.

        In Star Wars, the Force IS out there, like water in a river and we are all little row boats bobbing in the current. --To manipulate the water, (the Force), you need something to stick in the water. Like midichlorians, the more 'Oars' you have to work with, the more you can alter how the Force affects you. (Sorry. That's a horrible metaphor

      • Re: (Score:3, Insightful)

        by Chris Burke (6130)

        The Force is everywhere, just as Yoda said. The ability for a sentient being to manipulate the Force comes only via midichlorians.

        There's your explanation.

        And yes, it's still retarded. Best to pretend that never happened.

    • Re: (Score:2, Informative)

      by Opyros (1153335)
      Yep. And there are other kinds of non-chromosomal bodies which transmit genetic information, too — see the Wikipedia article on Extranuclear inheritance [wikipedia.org], to start with. And this has been known for a very long time; the book I just used to check my recollection of this was copyrighted in 1970!
  • by EEPROMS (889169) on Tuesday November 11, 2008 @07:24PM (#25727445)
    Who would have thought God coded DNA using Perl...
    • Re: (Score:3, Informative)

      by RuBLed (995686)
      You forgot the link [xkcd.com]
    • Re: (Score:3, Funny)

      by rrohbeck (944847)

      Come on, intelligently designed Perl is quite readable.

    • Well, we thought She was doing it with regexes, some of them a thousand characters or more long, but still basically pattern matching. But now it turns out that She's doing some of it with evals and self-modifying code, which opens up an entirely different beastiary. And who can guess what other clever little tricks She is using?

      The gene is dead. NYT confirms it...

  • Since the genome doesn't contain all the information that a person inherits biologically, what should we call the full package of inherited RNA, proteins, bacteria cultures, and who knows what else?
    • Imagine: a little molecular salt on that embryo, and we could make Johnny a genius and 7 feet tall!!

  • ...or not (Score:4, Interesting)

    by Relic of the Future (118669) <dales@digitaFREEBSDlfreaks.org minus bsd> on Tuesday November 11, 2008 @07:30PM (#25727511)
    Don't take my word for it, take the word of a cellular biologist [scienceblogs.com].
    • by tobiah (308208)

      He doesn't really refute anything in TFA, he just complains that this is old news, and gives his own summary.

  • by PineHall (206441)
    I did not really understand how complex and complicated the whole genome is. It is not a surprise then that I am a mess.
  • In Soviet Russia, YOU encode your own DNA!
  • This is why... (Score:3, Insightful)

    by jd (1658) <imipak@yaCOLAhoo.com minus caffeine> on Tuesday November 11, 2008 @07:42PM (#25727641) Homepage Journal

    ...I'm not (yet) convinced of the value of the gene-mapping you can currently buy. $1000+ and you get back a description that is essentially meaningless because they don't really understand how the genes work yet. You get tested for a handful of conditions which have genetic links, but not all. (Genetic studies have shown there to be 7 forms of ME, according to the specific genetic cause, but very few labs will test for any of them yet.) Without knowing more about how genes work, it is impossible to know if what these studies reveal is even an accurate reflection of the genetics behind such conditions.

    Alongside that is an argument in the reverse direction. If genes are not necessarily contiguous and/or can have ill-defined boundaries and/or can have components off the main DNA itself, then there is a definite possibility that there may be additional regions that could be useful for deep ancestry and genealogical DNA testing. This could help enormously as current research is pushing the limits of what is knowable using the regions and markers that are currently available. Entire haplogroup trees have been redefined because new information has revealed flaws in the previous models. More data, preferably more data that changes slowly, could be useful in getting these models right rather than continuously patching them.

    • by swid27 (869237)

      Entire haplogroup trees have been redefined because new information has revealed flaws in the previous models.

      Not just that, but the redefinitions have come about in large part due to the efforts of hobbyists [webalice.it] (the YDNA SNPs spreadsheet).

  • by cutecub (136606) on Tuesday November 11, 2008 @07:48PM (#25727683)

    I recall people freaking out when the human genome project revealed that Humans only have about 30,000 genes rather than the previous estimate of 150K.

    It always seemed to me that measuring Human complexity based on the number of our genes is a little like judging a book by the number of words it contains. It completely ignores the fact that words have Meaning.

    Poetry is both the most compact and the most subtle form of written expression.

    This latest finding suggests to me that something similar applies to our genetic heritage.

    -S

     

    • Re: (Score:2, Funny)

      by Anonymous Coward
      I'm sorry to say,
      your genes are a complete mess
      and not poetic.
    • by Chris Burke (6130) on Tuesday November 11, 2008 @08:28PM (#25728061) Homepage

      I recall people freaking out when the human genome project revealed that Humans only have about 30,000 genes rather than the previous estimate of 150K.

      It always seemed to me that measuring Human complexity based on the number of our genes is a little like judging a book by the number of words it contains. It completely ignores the fact that words have Meaning.

      Uh, I remember when they discovered that too, and I don't recall any scientists "freaking out" because the low number of genes implied we had low "complexity". Instead, I remember them being very excited, because they already knew there are far more than 30,000 proteins generated from our DNA, meaning that the 1:1 gene:protein mapping theory had to be wrong, and the mechanism was far more complicated than previously thought.

      This sounds to me like a continuation of the line of inquiry opened by that discovery years ago, where now they're gaining a better idea of how the genes really code for proteins. With the extremely interesting aspect that some of this is controlled by things not part of the DNA itself, yet which can still be inherited.

      To (ab)use your analogy, if the human body is a work of literature then proteins are the words, and genes are characters. The number of words hasn't changed, it's just that before we thought the language was like Chinese, where a single character mapped to a single word. Now we realize it's more like English, where the interactions between characters create different words. Oh and now we've discovered that there's also punctuation like apostrophes and hyphens which can significantly alter the meaning of the resulting words.

      • by Artifakt (700173)

        I don't recall the professionals as a whole 'freaking out' either, but when that 30,000 number began being bandied about, there were scientists who pointed out that some other species seemed to have a lot more than 30,000 genes (some amphibians in particular, had anomalously high numbers). I also recall comparisons to the numbers found in fruit flies, which led to comments that either fruit flies were a lot more complex than we had thought, or there was something else very strange going on.

    • Re: (Score:2, Interesting)

      by evolvearth (1187169)
      The debate was philosophical at the heart of it, because at the root of the debate was the problem of nature vs nurture. Many happy about the discovery were using it ease their fear that human behavior could be traced to genes.
    • Where you start in a code has an awful lot to do with the output, or if it runs at all. First of all, there are base triplet "synonyms" aplenty since there are many more base triplets than there are amino acids. This means there are a variety of ways to code the same protein, so it is possible to tweak a sequence without changing its function. What if you were to start some number of base pairs into a sequence -- might it also code for a valid protein? Would changing a base pair change the output of this ne

  • Can't be harder than programming a graphics card.

  • An analog? (Score:3, Interesting)

    by jlowery (47102) on Tuesday November 11, 2008 @08:02PM (#25727831)

    Does anyone else see the resemblence between DNA and crufted up old legacy software? Concepts about how heredity works get turned on their head once the mechanisms are examined in detail. I expect next it will be discovered that there are bugs in the DNA transcoding that are fixed by patches which in turn have patches.

    • Does anyone else see the resemblence between DNA and crufted up old legacy software?

      Well, imagine that this software started out as a simple "hello-world" program, and that every time the requirements changed -- a frequent occurence -- it was updated by repeatedly making the smallest change required to bring it a bit more in line with the requirements, with no regard at all to readability or maintenance. Further assume that random changes are being made all the time, and are only removed when a customer registers a complaint.

      The result would probably look something like DNA.

      • by jlowery (47102)

        Actually, I was thinking of something even more confounding: superficial "fixes" that cover up an underlying problem, such that the the core problem can never be corrected because to do so will break the patch (and the patch of the patch). I see that sort of thing occurring where I work. (I'd run screaming, but they keep throwing benefits and bonuses at me. I sometimes wonder if I still have a soul.)

    • Re: (Score:3, Interesting)

      by tfoss (203340)

      I expect next it will be discovered that there are bugs in the DNA transcoding that are fixed by patches which in turn have patches.

      Already [icnet.uk] discovered [wikipedia.org].

      -Ted

  • The term 'gene' has undergone quite a bit of change in its history, so this isn't really all that surprising in light of this. The term was originally coined (probably by Mendel himself, but I don't remember) to mean roughly "whatever is responsible for the observable results of hybridization experiments" and later, with the advent of molecular biology, came to be shorthand for referring to a molecular structure of a certain kind. It's an interesting question of course, whether those definitions are coext
  • by servognome (738846) on Tuesday November 11, 2008 @10:36PM (#25729077)
    RE: NOTICE OF COPYRIGHT INFRINGEMENT

    Ladies and Gentlemen:

    We act on behalf of God (the "Owner").

    As required under Sections 512(c)(3) and 512(d)(3) of the Digital Millennium Copyright Act (17 U.S.C. ??512(c)(3) and 512(d)(3)), we are instructed to place you on notice that:

    1. The Owner is the exclusive owner of the copyrights in and to the human DNA, RNA, and all other information contained therein

    2. Decryption of aforementioned encrypted information constitutes an unlawful cicumvention of encryption technology

    Please cease and desist from further decryption of stated copyright information and publication of previously acquired DNA information.
  • by MrKaos (858439)
    I thought there was only one Gene Simmons, who does he think he is, Sting, Flea?
  • Makes sense (Score:3, Funny)

    by Drakkenmensch (1255800) on Wednesday November 12, 2008 @08:55AM (#25732213)
    I guess science is coming up with a better explanation every day why your neighbour's youngest boy has the milkman's hair color!

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