Forgot your password?
typodupeerror
Biotech

Human Genome More Like a Functional Network 304

Posted by samzenpus
from the nothing-wasted dept.
bshell writes "An article in science blog says we may have to rethink how genes work. So called "junk DNA" actually appears to be functional. What's more it works in a mysterious way involving multiple overlaps that seems to be connected in some sort of network." From the article: "The ENCODE consortium's major findings include the discovery that the majority of DNA in the human genome is transcribed into functional molecules, called RNA, and that these transcripts extensively overlap one another. This broad pattern of transcription challenges the long-standing view that the human genome consists of a relatively small set of discrete genes, along with a vast amount of so-called junk DNA that is not biologically active. The new data indicates the genome contains very little unused sequences and, in fact, is a complex, interwoven network. In this network, genes are just one of many types of DNA sequences that have a functional impact. "Our perspective of transcription and genes may have to evolve," the researchers state in their Nature paper, noting the network model of the genome "poses some interesting mechanistic questions" that have yet to be answered."
This discussion has been archived. No new comments can be posted.

Human Genome More Like a Functional Network

Comments Filter:
  • by thogard (43403) on Thursday June 14, 2007 @12:11AM (#19501109) Homepage
    Its what we in the programming field would call the Data Segment.
    • Re: (Score:3, Insightful)

      by buswolley (591500)
      I doubt it. Analogies always fall down.
    • by Founder of PostGenet (927571) on Thursday June 14, 2007 @12:42AM (#19501269)
      The genome is fractal - governing fractal growth of organelles, organs and organisms. Even from a single fractal template (e.g. the algorithm of z=z^2+C) an enormously "complex" pattern, full of self-similar repetitions will develop. The "gene"-parts of the genome determine "fractal templates" of proteins, while the "PostGene"-sequences supply the auxiliary information necessary for iterative hierarchical development (architecture of complex protein structures). This concept/utility (FractoGene) triggered 300+ entries in slashdot in 2002 when an algorithmic approach first challenged the "gene/junk" dogma. The saga (including slashdot reference) is recorded at http://www.junkdna.com/ [junkdna.com] (as well as on http://www.fractogene.com/ [fractogene.com] ) Of course it is not junk... "junkDNA" is not a scientific term any more - but an important nickname for "the biggest mistake in the history of molecular biology". pellionisz_at_junkdna.com
      • by Grail (18233) on Thursday June 14, 2007 @01:35AM (#19501551) Journal

        In laymans terms, the "Junk DNA" provides the bootstrap routine and program code of an life form building nano-machine. The "Gene DNA" provides the instructions to the life-form-building-machine on how to make this life form a "human" or "fly" or "bacteria".

        Papers such as A minimal gene set for cellular life derived by comparison of complete bacterial genomes [pnas.org] provide some first steps into understanding how all this DNA works together.

        And to the grandparent post - I would argue that the "junk DNA" is not the data segment. For decades we've been thinking of the "Gene DNA" as the program when it is in fact the input data, while the "Junk DNA" is the boot loader, operating system and interpreter. But the machine doesn't build stuff and then move on (like a human-built factory) - it replicates itself, subtly altering the replicants to become more specialised along a growth path that will make one new machine produce stuff that will eventually become a femur, while the other new machine starts building stuff that will eventually become a gluteus maximus.

        I've heard of a project where a company set out to create a synthetic bacteria based on the minimal possible DNA, which they could then patent, and use as a base for testing genome manipulation or gene therapy or some such nonsense. Not sure if that's fact or fiction though.

        • by MikShapi (681808) on Thursday June 14, 2007 @02:08AM (#19501731) Journal
          Not quite. Your analogy appears somewhat broken.

          Here's the question - is non-gene DNA /machinery/ or /DATA/?

          If it's the latter, junk DNA would be conceptually closer to filesystem metadata (and maybe even "free diskspace" in as far as introns etc. go) than the OS.
          I fail to see how it bootstraps anything. A DNA molecule does not to my best knowledge start proliferating on its own when put on agar. Cellular facilities are required. True, you build said cell facilities from data stored in genes, but still I can't find any underlying principle shared by the bootloader, OS or whatever interpreter on my computer and my non-gene-coding DNA.

          FWIW, I'm a coder, a unix sysadmin and a (somewhat late-aged) biochem undergrad student, so feel free to dive as deep as you like into a technical comparison. I've been playing with comparison models of my own for a while (all of which have the annoying habit of breaking at one point or another) and am intrigued to hear more ideas on this.
          • by xenocide2 (231786)

            Here's the question - is non-gene DNA /machinery/ or /DATA/?

            Non-gene DNA is data -- ribosomes and RNA polymerase are the machinery. I like to think of them as compilers. Chemistry is the real computer, ribosomes etc are among the most important programs. Interestingly, they're sophisticated enough to "compile" themselves, I think. There's some level of control in the data itself as to what gets transcribed: promoter and inhibitor sequences, introns and exons all control what gets transcribed, and there's undoubtedly more and higher levels of expression regulation g

            • by Magada (741361) on Thursday June 14, 2007 @05:33AM (#19502693) Journal
              Nonono... any LISP programmer could have told you this... the code IS the data. And viceversa, ofcourse.
              • Re: (Score:3, Funny)

                by Walt Dismal (534799)
                Actually, that is pretty relevant to brain operation where neural networks both store data and compute.

                But on to my original reason for posting. If some kind of networks are involved in DNA operation, three ideas come to mind: 1) genetic spam 2) denial of DNA service attacks (I think viruses kind of do that in a way. Making them biological black-hat hackers), and 3) if the RIAA even THINKS of suing me for copying DNA, next time I catch the flu, I'm going to cough ALL over their lawyers. DMCA THAT, yoo ho

          • Re: (Score:3, Interesting)

            by gr8_phk (621180)

            Here's the question - is non-gene DNA /machinery/ or /DATA/?

            How about this:
            The non-gene DNA is software - i.e. the CODE segment.
            The gene DNA is data - the DATA segment - and defines how to build specific molecules.
            The cell and its internals are the hardware.
            All IO is through chemistry - i.e. concentrations of various molecules.

            There are more things scanning DNA than the repair devices aren't there? Could some of these things be interpreters of some sort? If they had the ability to "write" a base pair

    • by TekPolitik (147802) on Thursday June 14, 2007 @01:16AM (#19501467) Journal

      Its what we in the programming field would call the Data Segment.

      Overlapping, independent sequences? It's quite obviously spaghetti code.

    • Wouldn't that be the other way around? The "junk" is the code segments, and the genes that code proteins are the data segments?
    • by gringer (252588)
      Given that they're suggesting that there's a high proportion of functional elements in this non-genic DNA, I'd be more willing to call it the Code Segment, and call the genes the Data Segment.
  • by Tablizer (95088) on Thursday June 14, 2007 @12:19AM (#19501149) Homepage Journal
    They need to hire some Perl and 60's-style-COBOL programmers who know how to read tangled code ;-)

    • by Savage-Rabbit (308260) on Thursday June 14, 2007 @04:44AM (#19502449)

      They need to hire some Perl and 60's-style-COBOL programmers who know how to read tangled code ;-)
      My experience with Perl developers is that writing tangled code isn't a problem for them. It's reading, even their own, tangled code that they find difficult. I sat down with a Perl guru where I worked some years ago trying to debug a particularly nasty piece of Perl code. The whole time he kept going on about "Who writes code like this!?!" until we looked it up in the CVS repository and it turned out it was he himself who wrote that particular block a few years earlier. Syntactic flexibility is nice but it has a downside.

  • Imagine a Beowulf cluster of...wait a minute.

  • by Panaflex (13191) * <convivialdingo@@@yahoo...com> on Thursday June 14, 2007 @12:24AM (#19501167)
    It's somewhat funny - I remember having this exact discussion with my genetics professor. I was a chem major who is now a developer.

    It seems to me that DNA/RNA is "machine code" and data which runs on the laws of nature. It's a layer removed from silicon design, more akin to a self-modifying FPGA.

    In other words we're so far only looked at the boot code and associated data. The "program" is what we were calling junk.

    And it makes sense - if you think of the program as a massive recursion network which builds common parts (stem cells) and then organizes and specializes.

    I know that's a simple bastardization ... but perhaps I've just looked at too much dissassembler. I will feel a little vinticated if this is proven.
    • Re: (Score:3, Insightful)

      by fermion (181285)
      Human constructs are often used as metaphors for biological systems. There is nothing wrong with this. Comparing natural systems to our own creations is simply one of our primary methods of understanding those natural systems. I, however feel, that the most significant understanding occurs when we start taking about how the natural system differs from human constructions.

      One of the more interesting examples of such metaphor is brain research, in which every IT advance has been put forth as the model th

  • by Nymz (905908) on Thursday June 14, 2007 @12:24AM (#19501169) Journal
    After assembling something, if there are any parts left over I simply declare them to be extra junk. With scientists declaring the same thing about DNA they can't identify, I guess the old saw is true, great minds do think alike.
    • by SnowZero (92219)
      And if there are holes or parts missing when you are done, just say they will be filled with dark matter.
    • After assembling something, if there are any parts left over I simply declare them to be extra junk. With scientists declaring the same thing about DNA they can't identify, I guess the old saw is true, great minds do think alike.

      They used to say that the pancreas was just there to keep the rest of the guts in place.
      They once removed a part of the brain that was obviously useless, and getting in the way of their operation to a vital part... the patient could never again acquire new knowledge after the operation (as in Memento).

      So I never believed them when they were saying "junk DNA".
      As usual, that was just hubris.

  • interesting (Score:4, Informative)

    by wizardforce (1005805) on Thursday June 14, 2007 @12:25AM (#19501173) Journal
    From the article:

    The collaborative study focused on 44 targets, which together cover about 1 percent of the human genome sequence. or about 30 million DNA base pairs. The targets were strategically selected to provide a representative cross section of the entire human genome.

    The ENCODE consortium's major findings include the discovery that the majority of DNA in the human genome is transcribed into functional molecules, called RNA, and that these transcripts extensively overlap one another.
    actually if I remember correctly, there are 30,000 known genes which produce about 100,000 proteins [a little more than 3 per gene] which span a much larger amount of DNA that actually codes for proteins. genes have been known to code for multiple proteins since the Human genome project was completed. It has also been known that certain non-coding regions of DNA are not useless but in fact code for things like ribozymes etc. The article also talks about non-coding regions acting as a source for new structures. that is to say that the non-coding regions mutate and are selected for or against over time to form new proteins/enzymes etc.
  • My patent for "a functional network of multiply overlapping genetic transcripts distributed in 'junk' DNA" is on its way to the PTO.
  • by GFree (853379)

    So called "junk DNA" actually appears to be functional.

    Well that just proves it once and for all - it's not junk, hence it was designed properly.
    Therefore, God exists! /runs /trips over cat

    FUCK! /kicks cat, keeps running
  • by timothydsears (167111) on Thursday June 14, 2007 @12:57AM (#19501361)
    These scientists have probably been looking at cells running in the debugger...
  • sneaky (Score:4, Funny)

    by Takichi (1053302) on Thursday June 14, 2007 @01:09AM (#19501423)

    Our perspective of transcription and genes may have to evolve
    well played ... well ... played.
  • Whenever I read something like this, I get a reminder how poor is biologists' comprehension of Computer Science, Information Theory, and languages. So, 90% of genes aren't "junk" after all. To anyone who does know something about the aforementioned topics, duh!

    First, evolution would weed that sort of thing out in a hurry. Two organisms with genes that achieve the exact same thing, but one has a more efficient encoding? No contest! And, yes, such is possible. DNA isn't some mystical "super" language.

    • by plunge (27239)
      No redudancy? We have MILLIONS of copies of the same short satelite sequence whose only known purpose seems to be to reproduce itself. This very article notes that most of what they found is HIGHLY redundant.

      And it is NOT obvious that parts of DNA that don't code for anything useful would be weeded out: there are any number of mechanisms by which this would be prevented, and actually very little incentive TO weed anything out in any case.
    • by Daniel Dvorkin (106857) * on Thursday June 14, 2007 @01:58AM (#19501671) Homepage Journal
      Whenever I read something like this, I get a reminder how poor is biologists' comprehension of Computer Science, Information Theory, and languages.

      Whenever I read a post like this, I get a reminder how poor is most techies' comprehension of biology, and more specifically, what biologists do.

      Third, why this obsession with zeroing in on a magic gene that causes X? Do they think the language of DNA is context free? Defects could indeed be expected to have no context, but for the rest-- which genes determine a person's blood type? Eye color? Skin color? Going about that task by trying to find the magic gene for something like that is like a person who never learned to read trying to figure out the plot of a book by trying to recognize patterns of letters.

      Okay, why do we care? Because finding the genes (note my use of the plural there) that influence certain traits is the first step toward understanding the overall processes that create them. Obviously this is most critical in the area of genetic disease, although it's interesting for everything else too. We've known for decades that most traits, including diseases, aren't controlled by a single "magic gene." What statistical geneticists try to do is find locations on the genome which have a strong relationship to the trait of interest. And we know perfectly well that there will be a whole bunch of these locations for most traits, and that some of them may represent genes and some may represent something else. The purpose is basically to give the wet-lab biologists something to zero in on.

      Second, two of the examples you chose -- blood type and eye color -- are really terrible ones for your argument, because genetically speaking they're very simple traits (two or three loci each, IIRC) and, at least in the case of blood type, we know exactly where they are in the genome. Eye color I'm not sure about, and skin color is a little more complicated, but not a whole lot more so.

      Please do not confuse the pop-sci "scientists seek gene for X" writeups with what really goes on in the world of genetic research. It has exactly as much to do with real science as TV portrayals of hackers have to do with real computing.
      • Re: (Score:3, Funny)

        by Mr. McGibby (41471)
        Whenever I read something like this, I get a reminder how poor is biologists' comprehension of Computer Science, Information Theory, and languages.

        Whenever I read a post like this, I get a reminder how poor is most techies' comprehension of biology, and more specifically, what biologists do.


        Whenever I read something like this, I get a reminder how poor is biologists' comprehension of Computer Science, Information Theory, and languages. And I am a Computer Scientist who worked heavily in genetic research.
    • by Grym (725290) * on Thursday June 14, 2007 @03:09AM (#19502059)

      Whenever I read something like this, I get a reminder how poor is biologists' comprehension of Computer Science, Information Theory, and languages.

      Be careful here--you might just show your own ignorance. "Biologists" is a very broad term that covers a vast array of topics. Sure, ecology might not require much knowledge of computers and information theory, but such things are required reading for fields like molecular biology or modern genetics.

      First, evolution would weed that sort of thing out in a hurry. Two organisms with genes that achieve the exact same thing, but one has a more efficient encoding? No contest!

      Not necessarily. Sure, that may be the case for single-celled organisms that rapidly reproduce, whose selective forces dictate sheer metabolic efficiency, but for multi-cellular organisms, like mammals, there's good reasons to believe that that simply isn't true.

      Evolution isn't like a programmer. It isn't some transcendental force guiding a species to some aesthetically "perfect" design. The result of natural selection frequently isn't the "best" solution but rather whatever happens to work. In fact, many times adaptations based upon the selective pressures of the present are, in time, ultimately maladaptive for the species. A classic example of this is the trait for the disease sickle-cell anemia in humans which originally served to offer slight resistance to malaria but otherwise causes health problems and even death.

      A more efficient genome doesn't necessarily mean greater fitness. Consider the following example. For a large multi-cellular organism, which do you think has more reproductive/survival significance: (1) a mutation that deletes a few bases of non-coding DNA OR (2) a mutation that brightens a metabolically-wasteful, colorful marking that attracts mates?

      Second, ever tried compressing a DNA sequence? They don't compress very well! Meaning, they don't have much redundancy.

      OR that they are mostly random. The current model of DNA/genetics states that most of the DNA in the human genome is non-coding, not (significantly) subject to evolution. As such, it gets shuffled around (i.e. randomized) during cross-over events and mutations. That being the case, one wouldn't expect it to be very redundant or compress very well.

      Third, why this obsession with zeroing in on a magic gene that causes X? Do they think the language of DNA is context free? Defects could indeed be expected to have no context, but for the rest-- which genes determine a person's blood type? Eye color? Skin color? Going about that task by trying to find the magic gene for something like that is like a person who never learned to read trying to figure out the plot of a book by trying to recognize patterns of letters.

      In short, because that's what's easiest. A holistic approach to genomics research like you're describing is not currently technologically, academically or economically feasible for a myriad of reasons. The science just is not there yet.

      As an aside, I suspect we'll start to see a more integrated approach to genomics once the relatively low-hanging fruit of the one-gene --> one-protein research lines are throughly covered. However, I wouldn't expect such things to happen in our lifetimes given the difficulty of that aforementioned task and the sheer profitability of more conventional approaches. But what do I know? I'm "just a biologist." =P

      -Grym

      • Re: (Score:3, Interesting)

        by Chris Burke (6130)
        The result of natural selection frequently isn't the "best" solution but rather whatever happens to work.

        Exactly, and it's a popular misconception that evolution is always about the "best" and anything that is 1% "better" is going to dominate. Which simply isn't true, or our appendix would have vanished long ago. The fact is that appendicitis isn't enough of a problem to select against it strongly. The appendix just doesn't help, so the genes to maintain it aren't selected for either, resulting in the sl
    • It has long been suspected that 'junk DNA' or 'non-coding' regions had some purpose, but is was not obvious what purposes or how. But some amount of gene regulation was definitely known, like promoter sequences.

      Whenever I read something like this, I get a reminder how poor is biologists' comprehension of Computer Science, Information Theory, and languages. So, 90% of genes aren't "junk" after all. To anyone who does know something about the aforementioned topics, duh!

      If they hadn't suspected it, multiple groups around the world wouldn't have worked on this thing for such a long time. It's one thing to have a theory, another to prove it, despite what creationists may say ;)

      First, evolution would weed that sort of thing out in a hurry. Two organisms with genes that achieve the exact same thing, but one has a more efficient encoding? No contest!

      Actually, generally no and genome sizes can very a lot. There are a great many thing

    • by gringer (252588)

      Do they think the language of DNA is context free?
      I'll let you know in about 10 years (that's at least as long as I expect it to take to answer that question). I'm very interested in exploring the language and grammar of DNA after I finish my PhD.
      • I imagine DNA is like Lisp with a GOTO statement. There's no separating the "data" from the "program," things jump around at random, the times when they don't jump randomly they end doing stuff like doubling back and re-executing the last 10 base-pairs, then last 9-base pairs, etc., as a weird form of compression, and every sequence is double redundant in case of damage, but triple obfuscated as well.

        Good luck! Let us know how it goes!
    • Re: (Score:3, Insightful)

      by Jasin Natael (14968)

      I think your understanding is a little naive... There *are* magic genes that do X. There are also pseudo-random sequences that we have found a use for, and there are, further, sequences we carry around that are malicious, or do exactly nothing. But we carry all these genes around anyway, because the cost of doing so is negligible, and the chance for quick modification is beneficial in a population crisis. To get an idea of the tasks geneticists face, familiarize yourself with the Brainfuck [muppetlabs.com] programming l

  • Junk DNA (Score:4, Funny)

    by narced (1078877) on Thursday June 14, 2007 @01:16AM (#19501469) Journal
    I walk down the street and see 100s of people who appear to be predominantly junk DNA.
  • Finding out that not all viruses cause "sickness," and that the RNA injection of "friendly" viruses is a source of evolutionary change.

    I'm guessing a lot of the "human genome" is *airborne*.

    --
    Toro
  • by comm2k (961394) on Thursday June 14, 2007 @01:51AM (#19501637)
    Why it was called junk before you'd ask? Because our definition of what is useful wasnt all that accurate.. just looking at so called open reading frames and declaring everything else to be junk does not work. There is also the problem with insertions in a gene sequence that are either not or alternatively used. There are plenty of sequences that are never translated (no proteins are made of it) BUT without them we would be missing a big chunk of regulators etc. 'Recent' findings like ribozymes, IRES elemtens, attenuation elements etc. are all not translated into a protein yet serve a very specific function. Some of this 'junk' also serves as a insulator / separator between various sequences. We may never be able to map every nucleotide to some function but declaring it junk from the get go was just looking to be proven wrong. Just look up NCBI and look for some good reviews on this topic ;)
  • Being one of the 0.1% of /.ers that believe God created mankind, (and that we have been in slow genetic decline ever since),
    I thought when this 'Junk DNA' was mentioned many years ago that given time, that opinion will be reversed.
    Thus there was an advantage to ID biologist who would have the opinion, 'cells are an incredible biological computer with beautiful design, this is great fun reverse engineering it all, and there won't be Junk DNA because that goes against God creating life, so lets keep looking f
    • Re: (Score:3, Insightful)

      Why flame? A different point of view can lead to a break through. You initial hypothesis doesn't have to be correct to discover something useful. And who knows, maybe some day God (pick your deity here) will reveal him/herself to us unbelieving humans and we'll be proven wrong. Unexpected things happen every day.
    • Re: (Score:3, Interesting)

      by anubi (640541)
      I believe likewise.

      For me, its an Occam's Razor thing.

      If I find a pencil on the sidewalk, the most obvious thing is someone dropped it.

      I see life, and am at awe of its complexity. I have to conclude something designed it. Jehovah - Yahweh - the name as I understand it is Hebrew meaning "to cause to be". The name of God. Fair enough.

      My problem is finding God. I mean God. Not religion.

      Religion is Man's doing. Even if it was done in the best of intentions. The Church has killed some fine scienti

      • by Gryle (933382)
        Religion is Man's doing. Even if it was done in the best of intentions.
        Based on what I've read in the Bible, I'd believe God implemented religion, specifically Judaism/Christianity. However I'd have to agree with you that, like always, Mankind has thoroughly mucked up God's handiwork.
      • I can respect your views on the classic Teleological argument [wikipedia.org]. Establishing that something like Aristotle's Unmoved Mover is reasonable is completely different than accepting the Genesis story. What drives me nuts is when someone starts like this and two paragraphs latter they end up discussing The Flood and why the Universe, Earth, Man and Man's Rib aka Woman are no more than a few thousand year old. Since this is where the grandparent post seems to be headed, I want to understand how anyone can use Oc
      • You found your belief in God on what is known as the Teleological Argument [wikipedia.org]. There are a number of formal reasons why this argument is a poor one. The wiki link I've given you is a good place to start learning why it's not good, and Richard Dawkins' The Blind Watchmaker" has a fairly exhaustive treatment.
      • Re: (Score:3, Insightful)

        by Abcd1234 (188840)
        I see life, and am at awe of its complexity. I have to conclude something designed it.

        Weird. If you ask me, what's truly amazing about nature is the mind boggling complexity and variation that has grown out of beautifully simple principles such as natural selection. If you ask me, that's *way* cooler and more impressive than some god-thing running the show for kicks. After all, a fractal, to the naked eye, looks unbelievably complex... and it's expressed with a simple formula. The same is true of someth
  • junk DNA (Score:2, Interesting)

    by jalet (36114)
    "junk DNA" reminds me of the mysterious "dark matter", or "god" or whatever words we use to name something we know nothing about and don't understand, to give them some sort of magical status. It would probably be better to call it "unknown DNA", or "DNA Incognita", or even why not "Here be Dragons", to better remind us of how ancient maps were conceived (answer : it took ages to "publicly" discover all continents and isles).
    One thing I'm sure is that Nature doesn't waste resources, only Humans do, so each
  • I remember hearing way back when that the Human Genome people were doing their job more quickly by only mapping the active DNA and skipping the "junk"... if that "junk" is in fact active, does that mean they have a lot more mapping to do? Or is my info just hopelessly out of date?
    • Re: (Score:3, Interesting)

      by aadvancedGIR (959466)
      Yes, and yes.

      Anyway, it made sense to focus on the almost-understood parts first since the mapping techniques were very limited (but far more efficient each year) and the task so massively huge it would have been stupid not to limit the first steps to a better understanding of the most easy purpose of the DNA, which is protein encoding.

      Fully understand the DNA will take decades, if not centuries, and maybe someday scientists could be sure some parts of the DNA are actually useless, but that "90% junk" looks
  • The last time something like this was announced the Intelligent Design wakos went crazy. E.g. if "junk DNA" contains meaning then Evolution is wrong because that whole theory is based on protein encoding genes. If there is some overall all control mechanisms outside of the genes then that can only be evidence of some intelligently designed mechanism.
  • Interesting. Not that I sort of expected something like it for a while.. though maybe not as a "functional network". There is so much going on or that could be going on in there, maybe we need to have simulations made like the ones that allowed circuits to program themselves wierdly/organically using induced currents, just so we can get a handle on the tricks that evolution may have drawn on. For example rereading a sequence with a byte offset. Incremental diffs (maybe some of this happens in polyploidal pl
  • "Dammit, Jim! I'm doing all I can. I'm a Doctor, not one of your shiny youngbuck Engineers!"

    "This creature has no recognizable central nervous system - no heart, lungs, kidneys, liver or even a simple brain that I can find. Maybe if I WERE an Engineer I could make sense of all of.......this..."


    If McCoy couldn't envision a connection between data networks and the human genome, what does that say about - Wait...he was an actor, right? Not a real doctor in the future...?

    Roddenberry has some explaining
  • The new data indicate the genome contains very little unused sequences and, in fact, is a complex, interwoven network. In this network, genes are just one of many types of DNA sequences that have a functional impact. "Our perspective of transcription and genes may have to evolve," the researchers state in their Nature paper, noting the network model of the genome "poses some interesting mechanistic questions" that have yet to be answered.

    If this research is right, it would be naive to assume it only appli

  • In DNA, looks like everything is a file. DNA doesn't have any pretty icons and we don't know how to read the metadata - if it exists - to identify the boundaries of an element and its function. Nor do we know if, within "file" elements - organised sequences of code - there are internal sequences using a different encoding. Is this surprising?

    The only thing that gives me huge pleasure in this (sorry) is that I find Richard Dawkins overbearing, overclaiming, and pompous. It's nice to know that his approach to

    • Do we know enough to be able to build a virtual machine to emulate the environment in which the Genome operates? In other words, can we feed the known genome in at one end and get a simulated person out at the end?
  • Does this imply that while certain characteristics depend very strongly on individual groups of molecules in a particular chromosome, in general our genetic information might be better thought of as somehow a property of the entire chromosome, analogously to thinking of the same chromosome's (relativistic) mass being a property of the entire chromosome rather than the algebraic sum of the parts?
  • The press release this story is based on is absolutely terrible, in that it's using a definition of "functional" that i can only describe as bizarre. The discovery in question is that much more of the genome is copied into RNA than we'd realized. According to the story, that makes it "functional."

    In reality, it only shifts the issue: we now have tons of RNA with no apparent function. That RNA is in the exact same situation that junk DNA was - in essence, we now have a junk RNA question. If that RNA tur
  • We've known for a while that DNA isn't just genes. For example, there are certain sequences associated with histones [wikipedia.org], and this has been known for a while (though I don't have the papers to site on me). Histones aren't functional in the same way most proteins are. They're more like DNA "spools" (thanks to wikipedia for this analogy). A human DNA strand is about 1cm long, which obviously is a lot bigger than the nucleus of a cell. So DNA coils up into a very tight structure in multiple layers of coiling. Firs
  • by jollyreaper (513215) on Thursday June 14, 2007 @09:09AM (#19503995)
    I'm sure it wasn't a responsible scientist who popularized the term, it was probably a science writer. But it's just a variation on the pointy-haired boss credo "Anything I don't understand is therefore easy" morphed into "Anything I don't understand is therefore unimportant or unnecessary." It's like that other popular fact, "we only use 10% of our brains!" No, we only know what 10% of it is doing.

    I guess this bugs me so much because I see the problems caused by an ignorance of the facts every day. "Hey, quit standing around! Let's git'r'done!" Yeah, charge into a situation like a bull in a china shop. Hey, asshole! There's a reason why we didn't want you to go through that wall, the cat-5 was back there! Wow, a new hire that I just found out about this morning? Why yes, we have no computer for him, we told you there's a reason why we have to be informed of hires once a position is announced.
  • by toby (759) * on Thursday June 14, 2007 @09:15AM (#19504061) Homepage Journal

    Machine simulation of genetic/evolutionary algorithms often produces so-called "junk" which when analysed further, this frequently proves to be tied to the function of the overall organism in mysterious ways. I'm sure that leading GA researcher John Koza made this observation in early papers, but it's something that anyone playing with genetic algorithms will encounter sooner or later.

    I couldn't find the quote I was looking for, but only this broad statement from Genetic Programming: Biologically Inspired Computation that Creatively Solves Non-Trivial Problems, Koza (1998):

    The design of complex entities by the evolutionary process in nature is another important type of problemsolving that is not governed by logic. In nature, solutions to design problems are discovered by the probabilistic process of evolution and natural selection. There is nothing logical about this process. Indeed, inconsistent and contradictory alternatives abound. In fact, such genetic diversity is necessary for the evolutionary process to succeed. Significantly, the solutions evolved by evolution and natural selection almost always differ from those created by conventional methods of artificial intelligence and machine learning in one very important respect. Evolved solutions are not brittle; they are usually able to grapple with the perpetual novelty of real environments.

This is now. Later is later.

Working...