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Earth Science

DNA Analysis Hints At a Fourth Domain of Life 124

Posted by timothy
from the not-even-counting-the-hereafter dept.
ecesar writes "The Economist is reporting on a recent paper published in the Public Library of Science, which suggests there might be at least one other, previously hidden, domain of life (besides eukaryotes, bacteria and archaea). Using DNA sequence data generated directly from environmental samples, the authors found sequences not yet seen in any cultured organism."
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DNA Analysis Hints At a Fourth Domain of Life

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  • So... (Score:1, Funny)

    by Anonymous Coward
    ...they discovered The Jersey Shore?
  • Obviously... (Score:5, Informative)

    by NecroPuppy (222648) on Thursday March 24, 2011 @10:39PM (#35607656) Homepage

    It's the seeds of life left by the Great Old Ones.

  • by mapkinase (958129) on Thursday March 24, 2011 @10:42PM (#35607674) Homepage Journal

    .. and I am underwhelmed.

    First figure does not identify (at cursory look) domains and the second figure shows "unknown" samples mixed up between bacteria and killer plasmids or between different branches of eukaryota.

    Frankly, I spent only a minute looking at this paper, so anybody who went deeper please share

    • Re: (Score:2, Insightful)

      by Anonymous Coward

      I too am underwhelmed, and irritated to have read the article. At first it sounded good, but this is clearly just some washed up douche looking for grant money claiming a new form of life without comparing sequences to any known virii (except the ones that actually matched it, which he dismisses), has made past mistakes in this exact line of research both business-wise and in the more recent time (which he cited, i don't know why) thinking this mystery new life he's searching for was something he later fou

    • Not underwhelmed here. It really is just a hint, as the title says. I spent a few minutes looking at it. At first sight, they could have been new sequences representing life forms from either of the three existing domains, or viruses. And, indeed, in the discussion section, they are careful with their explanations. The last two of four are deemed the most plausible.

      "[...] A third possibility is that the genes from novel subfamilies come from novel heretofore uncharacterized viruses. Given that the known viral world represents but a small fraction of the total extant diversity, and given some of the unexpected discoveries coming from viral genomics recently, this is entirely possible. For example, viruses have been characterized with markedly larger genomes that contain not only more genes, but genes previously found only in cellular organisms. In some cases, the viral forms of these genes appear to be phylogenetically novel compared to those in cellular organisms.

      [Explanation 4:] It has not escaped our notice that the characteristics of these novel sequences are consistent with the possibility that they come from a new (i.e., fourth) major branch of cellular organisms on the tree of life. That is, their phylogenetic novelty could indicate phylogenetic novelty of the organisms from which they come. Clearly, confirmation or refutation of this possibility requires follow-up studies such as determining what is the source of these novel, deeply branching sequences (e.g., cellular organisms or viruses). Then, depending on the answers obtained, more targeted metagenomics or single-cell studies may help determine whether the novelty extends to all genes in the genome or is just seen for a few gene families."

      Most likely, these new sequences are from viruses, but I can't suppress hoping that there really are more domains out there.

      • by mapkinase (958129)

        Why do they make always the most exciting claim in the article? It's not like they are selling something, right...?

        Oh, wait...

        • I don't see any claim. Only a hypothesis. And what's wrong with an exciting hypothesis? I'd like to know, from you, why their hypothesis is implausible.

          • by mapkinase (958129)

            "Hypotheses non fingo"

            • I hypothesise that, if everyone, like Newton, would not have hypothesized, science would not have advanced much as it would have today. And on a personal note: what a pompous bore he must have been.
    • So the authors present the results of a new method for looking at all of the sequence data obtained by sequencing environmental samples.

      I.e., step 1, get some sea water or some ocean samples, step 2, sequence them all at the same time (so you could have many organisms present), and step 3, use methods (this is mainly what the paper is about) to figure out the genetic information of the organisms present. They are looking only for a few protein cDNA sequences (recA and rpoB and homologs) and small subunit
  • DNA is limiting (Score:4, Interesting)

    by mbone (558574) on Thursday March 24, 2011 @10:42PM (#35607678)

    The Venter approach is something akin to taking a library, putting the whole thing through a paper shredder, and trying to figure out how many languages there were in the library from a statistical analysis of the groupings of the letters on each piece of paper. It is marvelous, but it has its limits.

    If there were true aliens among us (microscopic organisms that did not use DNA for genetics), the Venter approach would not see them. I do not know of a good way to luck for such creatures, but I wish someone would figure one out, and apply it to something like Venter's samples.

    • by Anonymous Coward

      A better metaphor would be randomly shredding the contents of thousands of libraries which are likely to have many duplicate books between their catalogs. This leads to fragments boundaries from a shredded copy of BookA from LibraryX unlikely to be exactly the same as the fragment boundaries for BookA from LibraryY, and thus algorithms can try to match the overlapping bits of partial-duplicate fragments to reconstruct large portions of whole books.

    • by Anonymous Coward

      I'm curious on what basis do you talk about such things?

      A. What Venter did not invent this approach it was merely one of the first large scale applications of 2nd generation sequencing (pyrosequencing).
      B. It is nothing like the analogy you gave of shedding a library to determine how many languages. Hint: less statistical analysis and more string matching to cultured (well known) sequences.
      C. Aliens that do not use dna completely misses the point of the articule.
      D. Funny story. The tube that Venter used to

    • I do not know of a good way to luck for such creatures, but I wish someone would figure one out

      Follow the rainbow to the end for the pot of gold.

    • by osu-neko (2604)

      If there were true aliens among us (microscopic organisms that did not use DNA for genetics), the Venter approach would not see them.

      Of course not. Nor is it what they were looking for, nor is it what is being claimed. But thanks for the complete non sequitur.

      I have a cookbook that explains how to bake an apple pie. This technique is also completely useless for finding microscopic organisms that don't use DNA. But it makes great tasting pie nonetheless. Criticizing it for failing to find non-DNA based life forms, but merely making great tasting pie, is a special kind of stupid...

    • Its not about detecting non-DNA life.

      The principle is that the main way that we detect microbial life is by culturing it. Take a sample, swipe some on agar on a petri dish, see what cultures grow. Take sample of culture, DNA test/examine under microscope etc, document and catalog. For added versatility try culturing with variations of medium, temperature etc.

      Unfortunately it might be that the majority of microbial life on Earth does not grow on the kind of cultures that we prepare for these experiments and

    • by jamesh (87723)

      The trouble is that if you widen your search for things that aren't DNA too, you are going to get a whole load of false positives. I bet every time lightning strikes it mixes up a whole bunch of molecules in such a way that they could in theory form part of some non-DNA (or even non-carbon) lifeform.

  • by 2br02b (448267) on Thursday March 24, 2011 @10:50PM (#35607716)
    One of the paper's authors has posted more details on his blog here http://phylogenomics.blogspot.com/2011/03/story-behind-story-of-my-new-plosone.html

    We do not have a conclusive explanation for the origin of these sequences. They may be from novel viruses. They may be ancient paralogs of the marker genes. Or they may be from a new branch of cellular organisms in the tree of life, distinct from bacteria, archaea or eukaryotes. I think most likely they are from novel viruses. But we just don't know.

    • by mapkinase (958129)

      Quite a different phrase caught my eye:

      This is a post about a paper that has been a long long time coming

    • It will likely be a virus. We have really only scratch the surface on virus, literally. At this time, nearly all of the ones that we have found at those that were QUICKLY symptomatic. Those that are quietly transferring genes amongst all eukaryotes or all prokarotes, are not even being looked for.
  • Yeah, you read the subject right. Bigfoot.
    • The four domains of life are as follows: eukaryotes, bacteria, archaea, William Shatner.
      • The four domains of life are as follows: eukaryotes, bacteria, archaea, Chuck Norris.

        There - fixed that for ya.

        • The four domains of life are as follows: eukaryotes, bacteria, archaea, Chuck Norris.

          There - fixed that for ya.

          No, there used to be 24 forms of life. Chuck Norris solved that.

        • No, everyone knows that Chuck Norris is the father of all life on earth. Except for the weak ones: those he merely tolerates their continued existence until such time as he must vent some of his rage through his foot.
  • How exactly are they defining this term? What constitutes an "environmental sample" to a geneticist or evolutionary biologist?

    • by mapkinase (958129)

      Basically it's sequencing ocean instead of organism (the latter is more complicated and thus does not have a future). Or human gut. Or soil.

      When identifying organism sequence analysis relies on many markers in many genes. Here it's not possible, because you have just separated genes from many organisms.

    • by jestill (656510)
      They went to the ocean, scooped up some water, and the sequenced it. In environmental genomic sampling, you target an environment for sequencing (biofilm, soil, water, the human gut etc) and not a specific genome (corn, rice, humans etc).
      • by macraig (621737)

        But in reading the Economist article, filters (and by extension pore diameter) were mentioned, so apparently they (Venter?) were intending to scoop up actual organisms. Is the difference that they don't care whether they're intact or distinct? Is that what characterizes an "environmental sample", where DNA of multiple species is muddied together, and likely just fragments? I know nothing of the techniques used to cull DNA from either distinct creatures or rough samples.

        • by reverseengineer (580922) on Friday March 25, 2011 @01:22AM (#35608304)
          Yes, for an environmental sample like this, the totality of the sample's DNA is isolated and sequenced together, producing a library of mostly partial genomes. The original Venter paper http://www.sciencemag.org/content/suppl/2004/04/01/1093857.DC1/Venter.SOM.pdf [sciencemag.org] (might require registration) about the expedition/ yacht cruise details the methods used to collect and extract the sample:

          Sampling on the RV Weatherbird II was done as follows: Seawater (170 liters) from stations 11 and 13 was directly filtered through a 0.8m Supor membrane disc filter (Pall Life Sciences) followed in series by a 0.22m Supor membrane disc filter (Pall Life Sciences). The sample from station 3 was pumped into a 250 L carboy prior to being filtered through the impact filters. The length of time from collection of the sample until the end of the filtration step was approximately one hour. Filters were placed in 5ml of sucrose lysis buffer (20mM EDTA, 400mM NaCl, 0.75 M Sucrose, 50mM Tris-HCl, pH 9.0) and stored in liquid nitrogen on the Weatherbird then placed at -80C until DNA extractions were done.

          Sample preparation. The impact filters were cut into quarters and placed in individual 50 ml conical tubes. TE buffer (5 ml, pH 8) containing 150 ug/ml lysozyme was added to each tube. The tubes were incubated at 37oC for 2 hours. SDS was added to 0.1% and the samples were then put through three freeze/thaw cycles. The lysate was then treated with Proteinase K (100 ug/mL) for one hour at 55oC followed by three aqueous phenol extractions and one extraction with phenol/chloroform. The supernatant was then precipitated with two volumes of 100% ethanol and the DNA pellet washed with 70% ethanol.

          Which is all to say that a large amount of seawater was filtered through filters of appropriate pore size to catch microbes, the cells were broken open and the proteins were broken down, and the DNA was extracted with alcohol. The DNA extraction procedure is pretty standard for anything whose genes you'd like to sequence; more commonly, the sample would be made of cells from a single species or organism, like a human blood sample or a bacteria cell culture, but in this case, the sample is a mixture of all of the microbes in 175 liters of seawater.

          • by macraig (621737)

            Thanks for that. I understand just enough of it to grasp the essential process now.

        • Yes, they scoop up many organisms, then extract DNA and sequence bits of it. Except for sequences which match the DNA of something already known, they can't tell what the organisms were, or which fragments belong together.

  • by MrEricSir (398214) on Thursday March 24, 2011 @11:01PM (#35607774) Homepage

    I mean there's life.com, life.net, life.org, life.co.uk...

  • by Ranger (1783) on Thursday March 24, 2011 @11:02PM (#35607778) Homepage
    for a lay audience. And did a great write up. Glimpses of the Fourth Domain? http://blogs.discovermagazine.com/loom/2011/03/18/glimpses-of-the-fourth-domain/ [discovermagazine.com]
    • by gblackwo (1087063)
      Interestingly, according to that article, the fourth domain of DNA consists of a group of viruses. So I guess this is getting close to that gray area of "What constitutes life".
  • What if that DNA comes originally from one of the known domains, but was somewhat damaged by chemicals/radiation/whatever sources so it couldn't be recognized as a normal one?
    • Re:Dnamaged ? (Score:5, Insightful)

      by Altrag (195300) on Friday March 25, 2011 @02:41AM (#35608558)

      Absolutely. However, there's a few caveats:

      - Each "damage" will only affect one specimen for any given damage pattern. The chance that two individuals of species get genetically damaged in exactly the same way is pretty slim.

      - If the "damage" is detrimental to the species, the genetic change isn't likely to last long on evolutionary time scales.

      - Each "damage" will only affect a small number of genes -- likely only one or two. Geneticists create families of species by comparing the various genetic similarities. So if you have two very simple viruses that have 9 of their 10 genes in common, there's a good chance that they're fairly closely related.

      - And even that one gene is probably only slightly modified (a C replaced with a T in the DNA or something along those lines), so there's an even deeper comparative level for genetic matching.

      The probability of a catastrophic genetic change to the extent that we couldn't recognize its origin still producing a viable creature is so unbelievably small as to be ignored -- at best, it would get lost in the midst of basic human error.

      Of course its theoretically possible. In the same sense that its theoretically possible for all of the atoms in your body to simultaneously quantum tunnel in exactly the right way such that you pass through the nearest wall in-tact.

  • Let's call it.... a "Memristorganism"
  • by Guppy (12314) on Thursday March 24, 2011 @11:48PM (#35607964)

    http://phylogenomics.blogspot.com/2011/03/story-behind-story-of-my-new-plosone.html [blogspot.com]

    They may be from novel viruses. The They may be ancient paralogs of the marker genes. Or they may be from a new branch of cellular organisms in the tree of life, distinct from bacteria, archaea or eukaryotes. I think most likely they are from novel viruses.

    I'm going to go with this last opinion as well, it's probably from some virus, which would account for the sequence wackiness. I'm wondering if they can construct some speculative primers and (without isolating the organism) start sequencing outwards from these novel sequences, maybe get enough to tell if it's a virus or a novel organism.

    • by Sulphur (1548251)

      http://phylogenomics.blogspot.com/2011/03/story-behind-story-of-my-new-plosone.html [blogspot.com]

      They may be from novel viruses. The They may be ancient paralogs of the marker genes. Or they may be from a new branch of cellular organisms in the tree of life, distinct from bacteria, archaea or eukaryotes. I think most likely they are from novel viruses.

      I'm going to go with this last opinion as well, it's probably from some virus, which would account for the sequence wackiness. I'm wondering if they can construct some speculative primers and (without isolating the organism) start sequencing outwards from these novel sequences, maybe get enough to tell if it's a virus or a novel organism.

      They nearly destroyed Skynet last time, but some of the Novell viruses survived.

  • by Jane Q. Public (1010737) on Thursday March 24, 2011 @11:53PM (#35607988)

    "... the authors found sequences not yet seen in any cultured organism."

    Hillbilly DNA. Will wonders never cease?

  • by slick7 (1703596) on Friday March 25, 2011 @12:29AM (#35608118)
    The fourth domain of life must be the politicians, they appear to be intelligent but are mostly flat-liners.
  • If there where a forth domain of life the method we have used would find it... if and only if.

  • Instead of researching the possibilities of this new data, possibly giving us insights into how life evolved on Earth, why don't we just clasp our hands in prayer and thanks for the wonders of Intelligent Design?
  • by wherrera (235520) on Friday March 25, 2011 @03:01AM (#35608618) Journal

    Plos One, the New Internet Age's online quicker-to-publish-than-verify journal.

    Its record: 10% genuine breakthroughs, 50% hype, and 40% bad data. (Caveat: the previous sentence may be bad data.)

    Your call on this one.

    • by pz (113803)

      Plos One, the New Internet Age's online quicker-to-publish-than-verify journal.

      Its record: 10% genuine breakthroughs, 50% hype, and 40% bad data. (Caveat: the previous sentence may be bad data.)

      Your call on this one.

      You are basing these assertions on what data? And PLoS ONE differs from other publications by how much in these figures?

      If 10% of a journal's papers were actual breakthroughs, that would be exceptionally high. If true, we wouldn't be debating the added value that journals provide, for all we would need to do is to point to that example.

    • If nothing else it gives the common layman a means of observing or testing out or otherwise becoming familiar with the concept of peer review, even if it is a flawed implementation of that concept. You would be surprised at how many non-Slashdotters do not understand, or, for that matter, have not even heard about the concept of peer reviewed science.
  • Take a soil or a skin sample we don't know the correct conditions to grow >%90 of the organisms in that sample you can lob them in jar of nutrient broth but some simply won't grow while others will out-compete everything. Saying found sequences not yet seen in any cultured organism is a bit like saying found paving slabs not seen under any streetlight.
  • I thought we already have four, in common terms: plants, animals, fungi and bacteria. So if something else is discovered it would be the fifth. No?
  • ...but not as we know it."

  • Humans have this notion their science as it is now, is 100% complete, and yet, when I know that there are so many new ways of seeing things, x-ray,ultraviolet,infrared, etc.... which have been developed in the last 50 years or so, you tend to think, there might be a few more spectrums we know nothing about, not even its existence, so why think that all we know is all there is, why not leave some room for discoveries, like this goo, its a 4th type of creation material, but there could be a 5th, 6th, 7th we d

    • by Yosho (135835)

      Humans have this notion their science as it is now, is 100% complete

      Uh, no? The only people I know who say science is "100% complete" are Bible-thumping creationists who are setting up strawman arguments. Any real scientist will tell you that what we do know is a drop in the bucket compared to what we don't.

      x-ray,ultraviolet,infrared, etc.... which have been developed in the last 50 years or so, you tend to think, there might be a few more spectrums we know nothing about

      Have you taken a high school physics class? The terms "x-ray," "ultraviolet," and so on are just arbitrary names we've ascribed to frequency ranges in the electromagnetic spectrum. There's an infinite number of potential frequencies, some of which are more useful tha

  • It's slashdotes, a more evolved life form that does not dwell in basements, nor subsist on Cheetos and actually has real relationships.

    No extant forms have been discovered.

  • ...this should be obvious??
  • It always irks me when the media gives Venter credit for the first Human Genome, when in fact Jim Kent at UCSC was the first to create a draft assembly.
  • Wernstrom!!!
  • Well, now we know where the creature in the black lagoon came from.

Biology is the only science in which multiplication means the same thing as division.

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