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Science

Scientists Discover Mechanism That Gives Shape to Life 138

Posted by samzenpus from the the-foot-bone-is-connected-to-the-leg-bone dept.
First time accepted submitter mcswell writes "Daniël Noordermeer and Denis Duboule, two researchers at Ecole Polytechnique Fédérale de Lausanne and the University of Geneva claim to have discovered how vertebrae get built in sequence in embryos (and by extension, how ribs, arms and so forth wind up in the right place). The story is that the DNA strands contain a linear series of HOX genes, and that the strands slowly unwind over a period of two days, successively exposing each HOX gene, thereby allowing it to be transcribed to form the segments of the vertebra. Snakes, it seems, have a defect that causes the system not to shut down; eventually it 'runs out of steam.' The same process is said to apply in many invertebrates, including worms (presumably segmented worms) and insects."
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Scientists Discover Mechanism That Gives Shape to Life More

Scientists Discover Mechanism That Gives Shape to Life

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  • Now if only we can find the gene that causes ignorance.

    • Now if only we can find the gene that causes ignorance.

      I think that's related to the HOAX gene. :-)

    • Re: (Score:2)

      by rtaylor ( 70602 )

      We are all ignorant. It would be challenging to find a single person who has all of the knowledge necessary to build a simple pencil (including extraction of raw materials; don't forget to include government applications to open the mine or take trees from the forest) let alone anything complicated.

      The question is, why do we express opinion on subject matter we are ignorant in.

      • Re: (Score:2)

        by lawpoop ( 604919 )

        The question is, why do we express opinion on subject matter we are ignorant in.

        Our ignorance is so profound we are oftentimes ignorant of it itself.

        • Hence the Italian proverb: Molto sa chi sa che non sa.

          -Much knows someone who knows he doesn't know.

    • Re: (Score:2)

      by PPH ( 736903 )
      The blond gene?

  • For the non-molecular biologist among us (Score:5, Informative)

    by GreatBunzinni ( 642500 ) on Sunday October 16, 2011 @09:39AM (#37730026)

    What a Hox gene might be [wikipedia.org]

    • thanks that was very helpful I thought 'shape to life' was metaphor of some sort. Not literally 'shape to life'.
  • Well, this is the creationist version of how snakes get their shape [blogspot.com] anyway

  • Hox genes are the basic sequence of embryogenesis (Score:5, Insightful)

    by wombatmobile ( 623057 ) on Sunday October 16, 2011 @09:57AM (#37730170)

    TFA is saying that organisms are built in slices, from the tip of the head down to the tip of the tail. These slices are activated in order, from first to last. It is the same in fruit flies, worms, whales, dogs, monkeys, deer and humans. The HOX genes control the basic sequence, like a player piano roll or a series of punch cards.

    The reason we get so many different organisms, like whales, fruit flies and elephants, is evolution [youtube.com].

    • Re: (Score:1)

      by fikx ( 704101 )
      I think the significant finding is how the layers are timed or sequenced....they knew that embryos develop in layers, they just didn't know how that was achieved. Now they do: layer after layer of the relevant DNA is exposed via a mechanical unwinding of the HOX genes.
      • This discovery also illuminates another aspect of growth. Sure, you can build in a slice fashion, but obviously the initial full structure will not have full internal (neural) communications, because that can only be grown point to point AFTER the points are built. So this explains why infant maturing involves such massive neural growth. The building has been constructed, now the phone and IT infrastructure gets built up, over years. Plus, the building keeps getting improvements and expansions, so wiring ha

        • Re: (Score:2)

          by d3ac0n ( 715594 )

          whoo-eee! Fruitful discovery./quote.

          Well, informative discovery would probably be more correct. NOW we will see if this discovery will actually bear fruit in finding therapies or the ability to correct for certain early birth defects such as Spinda Bifida.

    • Organic 3D printing, okay. The printers are cheap but you have buy 18 years worth of expensive ink cartridges in a manner of speaking.

    • "The reason we get so many different organisms, like whales, fruit flies and elephants, is evolution" That's irrelevant here.

      As for the article, the most interesting part is that instead of traditional regulation, where genes are turned on and off by specific interactions of gene area with other molecules (proteins, microRNA), the authors propose a mechanical mechanism where active and inactive HOX genes are spatially segregated in two blobs of DNA.

      The question is what mechanism provides persistent of this

  • It's in Science 'cuz now we can SEE it? (Score:5, Interesting)

    by enderwig ( 261458 ) on Sunday October 16, 2011 @10:27AM (#37730346)

    A caveat as I write this critique, I have only read the linked article and the abstract of the original scientific article, not the full Science article.
    Also, I'm a Ph.D. in Developmental Biology from 2000.

    If unwinding the super-coiled DNA is considered the chronometer for embryonic segmentation, what makes the DNA unwind at such a specific time? I'm not sure how much new light is shed by this work. We've known for >20 years that transcription factors help "open" DNA for the transcription process. We've also known for >20 years that HOX genes in their clusters are the masters of structural differentiation. Put these two facts together and we can see it should be obvious that the HOX genes need to be "opened" sequentially.

      In the end, we are left with the still burning question of "What controls the HOX genes and their clusters?"

    • Re: (Score:2)

      by mikael ( 484 )

      Maybe it's like MIDI file format for music - there are actually instructions that specify specific time delays. Other instructions activate and deactivate notes for particular instruments. Though it doesn't actually specify what an instrument should sound like. That's the job of the other data files, known as SoundFonts.

    • That's kind of what I was thinking, too. I remember reading years ago about experiments w/ HOX genes (I think) where they were able to get flies' limbs to grow out of their eyes and things like that. This doesn't seem like too much of an advance to me.

    • Re: (Score:3)

      by Suiggy ( 1544213 )

      According to a purvey of information posted on Wikipedia, Hox transcription factor proteins produced from the expression of the Hox genes activate the transcription of specific genes while at the same repressing the expression of other genes. Hox proteins are themselves regulated by other genes, such as gap genes and pair-rule genes, and there's a transcription factor cascade which controls the whole process for each stage, which has been explored in depth. Apparently, there's been a lot of work in this fie

      • Re:It's in Science 'cuz now we can SEE it? (Score:4, Informative)

        by Samantha Wright ( 1324923 ) on Sunday October 16, 2011 @12:38PM (#37731242) Homepage Journal
        That may sound novel and exciting, but what you've described is how every transcription factor works. enderwig was making a point about the timing mechanism. If you leave a transcription-driven genetic circuit to keep its own clock without any assistance, it generally does a pretty bad job. There has to be something fairly elaborate guiding the chromatin unwinding.

        • Precisely. From the abstract and press release, the authors imply that the opening of the super-coiled DNA is necessary and sufficient for the HOX genes to be temporally regulated. Now parsimony and K.I.S.S. usually are the correct ways of thinking about things, but based on what we already know from 10 years ago, simple unwinding can not be the temporal mechanism.

          tl;dr summary: We still don't know what starts the cascade of temporal regulation. I don't think this work moves us very far upstream in the regu

          • I might argue otherwise—if we can visualize the shifts in effect with this much precision, we can use bioinformatics and chemical kinetics to work our way backward and find what's generating the signal, both tasks that are comparatively well-solved.
    • From Wiki [wikipedia.org]
      Non-coding RNA (ncRNA) has been shown to be abundant in Hox clusters. In humans, 231 ncRNA may be present. One of these, HOTAIR, silences in trans (it is transcribed from the HOXC cluster and inhibits late HOXD genes) by binding to Polycomb-group proteins (PRC2).[19] The chromatin structure is essential for transcription but it also requires the cluster to loop out of the chromosomal territory.


      -KI

    • (reposting as myself, sorry.) Attempts to explain the mechanics of DNA leave me with so many burning questions I end up as a bemused pile of ash with some ACGT letters in it. Besides "What controls the HOX genes and their clusters?"

      • Article says When the time is right, the strand begins to unwind, so is there another clock that turns on this clock?
      • the genes encoding the formation of cervical vertebrae come off the spool and become activated . Beware passive voice, what activates them?
      • Does the HOX clock ru

      • so is there another clock that turns on this clock?

        My guess is yes, there is something else. It may not be a protein but a small nuclear RNA.

        but when new cells form in that area weeks later, how do they know their place?

        Molecular landmarks sort of like what makes one intersection different from another even if both have a coffee shop, a fast food place, and a gas station. The landmarks could be on the cells, on the extracellular matrix, a diffusable protein gradient, or some other way to differentiate an environment.

        Is the HOX system reused to control the layout of my arm down to five jointed fingers? If not, what takes its place at lower levels?

        Actually, they are. Nature likes to re-purpose genes temporally and spacially to do more than 1 thing when in the correc

      • "Does the HOX clock run in every cell? If not, which ones? If each one, what keeps them in sync? Some cells are 3 days old during this process, some are brand new"

        I'm the original OP, and yes, I wondered about this too--particularly how the current unwinding gets transmitted down the length of the animal as the cells undergo mitosis. Or maybe it only unwinds a little with each division, and only the cells at the posterior end (which I presume are in the last segment produced) govern further division? Exce

    • A few years ago I found out that the explorers in the science of paper folding have proposed that any three dimensional physical object can be formed by folding a single sheet. That resonated with my contact with embryology (which included watching frog eggs divide under a stereo microscope). And it still resonates with my work with special education kids where I puzzle about which layers of their motor skill function stack are not working well.

      So another burning question, or at least request for explanatio

    • It's the first step. I did not read the full article either, only browsed Figures, concentrating on Fig.3 (which is clearer for general audience, my biology-related Ph.D. is much further from the subject) but as far as I understand they discovered a sequence of regulatory events. I am not sure how new this is. From your remark it looks like it is not a big deal.

  • Snakes (Score:5, Insightful)

    by TeknoHog ( 164938 ) on Sunday October 16, 2011 @10:32AM (#37730378) Homepage Journal

    The sinuous body of the snake is a perfect illustration. A few years ago, Duboule discovered in these animals a defect in the Hox gene that normally stops the vertebrae-making process. “Now we know what’s happening. The process doesn’t stop, and the snake embryo just keeps on making vertebrae, all identical, until the process just runs out of steam.”

    Looks more like a feature than a bug to me. Another fine example of evolution by mutations.

    • Re:Snakes (Score:4, Funny)

      by Anonymous Coward on Sunday October 16, 2011 @10:43AM (#37730458)

      The real amazing discovery is that snakes run on steam!

    • I've heard a snake can grow a new tail if you cut it in half, while humans can't grow a new spine if you cut them in half. If that's true, one could argue that it's the humans with the defect.
      • Cutting a snake in half would kill it. They have vital organs along almost the full body length, and it'd bleed to death anyway. Perhaps if you just cut the tip of the tail off, though... equivilent to amputating a human's legs.

        • Not even the tip. When moving our snake's tank a short distance (a little Western Ribbon snake, essentially a fancy-looking garter snake), a piece of her tank furniture fell over and severed the tip of her tail (maybe half an inch). I can assure you it didn't grow back.

          It did continue to flex and jump around the tank for a minute or so, which was interesting. And FYI, the snake did OK, she hardly bled at all and was back to normal within a few days. We did consult our vet. :)

      • They can't. You're probably thinking of worms.

        The only vertebrate with a (very limited) form of limb regeneration is the salamander, and that's an amphibian, not a reptile like the snake.

    • Re: (Score:1)

      by Anonymous Coward

      Looks more like a feature than a bug to me.

      Not when you're on a plane!

    • Re: (Score:1)

      by Tablizer ( 95088 )

      "Run out of steam" is not very specific, including in TFA. That's the kind of thing I'd put on a biology test if I forgot the details.

    • Re: (Score:2)

      by Empiric ( 675968 )

      Teleology called. They'd like their terms "defect", "feature", and "bug" back.

      So does Genesis 3:14, but that's a whole different can of... snakes.

  • So snakes suffer from (Score:1)

    by Anonymous Coward

    an infinite loop error?

  • Defect? (Score:1)

    by Anonymous Coward

    Given how old and successful snakes are as a life form, I'd hardly call this a "defect". Just a "fascinating difference" in how the genes are expressed.

  • it will grow from the top to the bottom, one slice at a time

    First the neck, then the thorax, then the lumbar, and so on,”

    I wonder how two headed snakes happen. According to TFA, I can imagine how a snake head could have two bodies, but I've never heard of that.

    • At a guess, the process initiates at two seperate locations (Perhaps even two seperate embryos), and continues as normal until the two developing spines make contact. At which point the chemical process can't distinguish between them, so they continue growing as a single spine.

    • Conjoined twins. In this case, you start out with two heads which then merge into a single body.

      • Conjoined twins. In this case, you start out with two heads which then merge into a single body.

        Can you have conjoined twins in an egg situation? Aren't each of the fertilized eggs isolated from each other by a membrane or incipient shell?

  • So what is the implication of the defective snake? What happens if we could repair this defect? Would it grow to encompass a different form? Or would it just be a shorter, fatter snake?
    I'm sure there's a joke to be made here somewhere...

    • Re:Snake? (Score:4, Informative)

      by Samantha Wright ( 1324923 ) on Sunday October 16, 2011 @12:42PM (#37731284) Homepage Journal

      It would either be short and fat, or dead because there wouldn't be enough room for its organs to grow. Either way, it wouldn't slither very well, and would be at something of a disadvantage.

      The use of the word "defect," as you can probably already imagine, is a very biased way of looking at things and will probably do more harm than good. Although, of course, at the time the mutation first appeared, when snakes still had non-vestigial limbs, it probably was at least partially something of an inconvenience.

  • I think stuff like this should be touted as proof of Intelligent Design... not to prove God exists but to reconcile American fundamentalist Christian ideas with science. And from there push the meme that God wants us to examine the world and understand his creation so we can bask in the wonder of His glory. Then maybe they'll ease up on trying to oppose science sometimes.

    Question: How do the Jesuits feel about biological science vs. intelligent design? I assume (with total ignorance of their ideas on the

    • Re: (Score:1)

      by 9jack9 ( 607686 )
      "I personally never thought that there was any conflict between evolutionary explanations of change in the natural world and Roman Catholic Christianity." From "Evolutionary Biology at Regis, a Jesuit Catholic School" at http://academic.regis.edu/mghedott/evolut.htm [regis.edu].

    • Galileo was a long time ago. The Catholic church, by now, has no beef with the well-settled science on Evolution, the Big Bang, etc.

      Although I'm not quite sure what process they use to decide which parts should be taken literally (i.e. the resurrection of Jesus) and which should be discarded as poor translations of ancient epics (the seven days of Creation, Adam and Eve, etc.)

      And it baffles me that any form of Christianity decided to include Revelation; whoever wrote that had clearly discovered some Magic

  • Wow!

    Decades ago, in ninth grade biology class, I asked my biology teacher how a Hydra (or other creatures) knows how to form its shape from cells, but he hemmed and hawed, and essentially would not admit that he did not know, or even that no one knew. We had been supposed to look at some Hydra in class, but they never arrived or something like that. I later studied Hydra in Ecology and Evolution grad studies, but people still did not quite know how they formed their shapes.

    A couple lessons there for me I gu

  • What if someone were to take a newly created snake embryo and repair that 'defective' gene before letting it develop further? Would it automatically develop four limbs and look more like a lizard? Whatever the result, if successful it might give us some more insight into how these fascinating creatures evolved.
  • Obligatory post by a plant biologist who is sick of the animal folks overgeneralizing their findings in press releases.
  • The 1st thing that comes to mind is the possibility we could construct things out of organic material now. Instead of cutting down a tree to build a house we could organize tree DNA to deliver a real tree house. Patent pending.
  • Does this mean that lawyers have mutated HOX genes that fail to unwind, thus leaving them spine-less?
  • So how do I get this gene to express itself as greater penis size?

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