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Earth Open Source Science

A Wikipedia-Style Tree of Life Emerges 72

Posted by timothy from the 'tis-but-a-seed dept.
The Christian Science Monitor reports on the newly announced Open Tree of Life, a freely accessible unified interface to, and archive, of biological taxonomies. In the current version, data from nearly 500 evolutionary timelines has been assembled into a single, searchable view of all known life forms; From the CSM report: Building the computer code and compiling the data took three years, and involved collaborators from Chicago's Field Museum of Natural History, the Web development firm Interrobang, the University of Michigan, the University of Florida, Duke University, and George Washington University. "Many participants on the project contributed hundreds of hours tracking down and cleaning up thousands of trees from the literature, then selecting 484 of them that were used to generate the draft tree of life," said Cody Hinchliff, a scientist from the University of Idaho, in the announcement.
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A Wikipedia-Style Tree of Life Emerges More

A Wikipedia-Style Tree of Life Emerges

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  • Kardashian? (Score:4, Funny)

    by chill ( 34294 ) on Sunday September 20, 2015 @02:41PM (#50562485) Journal

    I can't find "Kardashian" in there. I figured it would at least show up under one of the various forms of uncultured bacterium.

  • Almost Cool (Score:4, Interesting)

    by JMJimmy ( 2036122 ) on Sunday September 20, 2015 @02:44PM (#50562513)

    It'd be cooler if it was general public friendly. Scientists might find it useful but the general public will have no use for something they can't understand. Really though it seems like they're just copying others databases (primarily NCBI and SILVA) which have "trees" of their own.

    • The Encyclopedia of Life is geared more toward the public http://eol.org/ [eol.org]. The cool thing about the effort in the open tree of life ( http://opentreeoflife.org/ [opentreeoflife.org] ) is that it is open data and open source driven. You can check out the code on github. https://github.com/OpenTreeOfL... [github.com]
      • I was going to say the same thing about eol.org. Why reinvent the wheel? I think eol.olg is very well done. Much better than wikipedia in terms of layout and navigation.

      • Yet it harvests much of the data from a closed RNA database...

    • It's more complicated than that. Opentree builds a taxonomy which is a 'consensus' from taxonomies from NCBI, SILVA, Index Fungorum, WoRMS, etc. This taxonomy is then used to scaffold the assembly of a phylogeny from the set of accepted trees. These trees (478 in the current synthesis) are selected from the ~3000 studies that have been contributed to the database. There are groups (for example spiders) where the coverage by available trees is rather sparse or absent. In these cases, the synthetic tree

      • It's like making an English dictionary, except way worse.

      • That's kinda my point. "wiki" style is really only useful if you have the general public involved. By harvesting the generic data (names/trees) from other databases all it's really doing is indexing sources scientists would already go to for the real data (ie: paywalled information). Without the real data behind it or something for the general public I can't see it being hugely useful to anyone imo.

        • The wiki aspect is the ability for anyone to upload a (published) tree and map its tips to names in the taxonomy. Literally, anyone with a github id can contribute. However, I do concede your point - the skill to map names to tips and access to trees are not attributes your average Joe is likely to display.
  • ...of multiple individuals of each species and to remain open sourced. Then we'll have a serious rush in biotech as algorithms designed for computational biology along the same lines of semantic footprinting will be able to act as an intermediary/compiler for writing genetic code.

  • But does it say on which day God created them?

  • Is there a prize? (Score:1)

    by Anonymous Coward

    ...for navigating from the top down to homo sapiens without using the search facility?

  • The Tree of Life can't Handle Open Source (Score:3)

    by tinkerton ( 199273 ) on Sunday September 20, 2015 @03:43PM (#50562823)

    Just the odd observation, but the treelike organisation is suitable for well defined species, in other words when lifeforms act pretty much according to closed source strategies (but not completely). According to some smart people in the beginning the dominant organisation was open source, lots of exchange.

    The open source thing still happens of course, and it's fascinating when it happens. It gets the news sometimes when the subject is Influenza.
    There was an important article almost 50 years ago (Symbiogenesis, see Lynn Margulis) stating that some components of the eukaryotic cell have actually been imported from prokaryotes: mitochondria and organelles.

    • Re: (Score:1)

      by Anonymous Coward

      Oh yeah, there were and still are loads of exchanges of functionality in biology.

      Parasitic organisms living off others, occasionally will accidentally become absorbed in to the DNA of the creature, or even in some cases deliberate like with retroviral strains.
      Some of these have even been linked to cancers whenever they become activated for whatever reason. (why they sometimes activate is something under heavy research right now ever since we found that out since it could provide a huge avenue of attack aga

    • Joking aside, most open source can't handle open source. I mean, you can't randomly insert emacs source code into the Linux kernel, can you? There are definitely rules that govern the exchange of source code between projects, even if we disregard the conflicting licenses. For example you often have to port code that runs beautifully on desktop GNU/Linux to run on a broken Linux like Android, and that's even if you're running the same architecture (x86, ARM, etc).
    • Yes, sometime the branches on the tree rub together and the consequences can be huge, such as when mitochondria 'decided' to take up residence in a larger cell and created the common ancestor of all animals. We don't know nearly enough about "open source" mutations to start mapping them, however if we took this tree and added genome sequences to the leaves and branch points, we might get some more hints.

      OTOH a "tree of life" doesn't really care about how the mutations occurred because 'species' is a some
    • I read that article in my college laboratory class!

  • graphical Harvard museum effort not available (Score:3)

    by call -151 ( 230520 ) * on Sunday September 20, 2015 @03:46PM (#50562841) Homepage

    It's really too bad that the fabulous museum exhibit display Deep Tree [harvard.edu] isn't more broadly available. There is a lovely display, with graphical interface, which is just enchanting to wander through much of the tree of life. It does a great job conveying the scale of the diversity of life and the boggling number of species, and it's aimed at the general public. It has nice pinch/zoom/etc. touch-screen functionality on a table-sized display. Unfortunately, for years, there was exactly one place on earth where you could play with it: at the Harvard Natural History Museum. And unless you are there at a particularly empty time, you will have to squeeze a fair number of kids out of the way to actually play with it for more than about two minutes. Now, things have improved a bit and it looks like there are a grand total of four museums [harvard.edu] that have the exhibit. (You should visit if there is one near you, try to avoid a time when school field trips are likely to be there!) The development was supported by a $2.3 million US National Science Foundation grant [nsf.gov] so public money was used to develop it, and it seems feasible to implement it or at least a scaled-down version of it on what are now much more common multi-touch displays like tablets or at least be available on the web, but as far as I can tell, it's been years since the grant and still the only place you can use it is in these four museums. I see this as a missed opportunity for a dramatic broader impact on understanding evolution and the scale of the diversity of life.

    • It's really too bad that the fabulous museum exhibit display Deep Tree [harvard.edu] isn't more broadly available. .

      Aha, happy to be mistaken and outdated on this one- I looked and found that now there is a web page via NOVA with a good interesting subset of the data. It's nicely done and at the DeepTree link at this link [pbs.org].

    • On my list of things to do should I ever inexplicably become astonishingly wealthy is to build a museum of phylogeny.

      It would be a natural history museum, but with exhibits organized phylogenetically and the phylogeny would be represented by lines (mostly on the floor but branching out onto walls where needed) with a scale of something like 1 meter to 1 million years. (There would need to be an ongoing process of updating as scientific consensus changes.)

      If you want to know how closely related you are to a

      • Re: (Score:2)

        by Sique ( 173459 )
        Will you have a building for the Gabonionta [wikipedia.org] about 2 km from the room for the H. sapiens?

        • That is really cool, I didn't know about those. Thanks.
          For the sake of practicality, they'd probably be 600m from H. sapiens in the Ediacaran building, plus there'd be little sign beside the path from 'origin of life' to the main museum, at 2 km, to mark the correct location.

        • Given that there is significant disagreement at this time over their placement in the TOL, or indeed whether they're even in the TOL (pity Dolf Seilacher died recently - a major contributor to the field.), then it's probably too early to plan where to put them.

          This museum had better have it's buildings on rails, so they can be shuffled around.

          • Re: (Score:2)

            by Sique ( 173459 )
            The age is quite undisputed, but the actual nature of the fossils is unclear: Are they really remainings of multicellular life, are they just some strange type of bacterial colonies, ore are are they abiotic anyway and thus don't belong in the TOL at all?

            I've been at the exhibition in the Naturhistorisches Museum Wien [nhm-wien.ac.at], and I've seen the fossils (or at least quite convincing replicas of them), and they looked like some type of small, round pillows with large braids. So to a non-palaeontologist like me, the

            • The age is uncontroversial (to me at least; I was reading up on these discoveries the last time I was working in Gabon, thinking I might take some vacation after work to rock - hunt these and the Oklo reactors. But Oklo is mined out and shutdown now, and the area had an Ebola outbreak. So I gave it a miss.)

              But with so many of these very ancient "fossils" you have to be extremely careful about misidentifying inorganic features as fossils. Witness "School's Embarrassment", the continuing dispute over "Moiz

              • Damn. HTML fail.

                I didn't know about the Vienna connection. If I had, I might have visited it when the wife and I were in the German Alps last year. I'll file that in the memory for future use.

          • Re: (Score:2)

            by Sique ( 173459 )
            For reference: That's the link to the actual exhibition [nhm-wien.ac.at] page.

      • When the American Museum of Natural History in New York redid the fourth floor exhibits about dinosaurs, they chose to arrange the specimens in a tree-like structure representing their phylogeny (well, subject to the constraint that it's basically a big loop with a few bumps and nooks and crannies.) At the time (this was the late 1990s,) it was controversial because most museums grouped specimens by function (carnivores, herbivores, etc.) instead of by their evolutionary path. In fact, the AMNH welcomin

  • Eukaryota > Opisthokonta > Holozoa > Metazoa > * > * > * > Bilatera > * > Deuterostomia > Chrodata > * > Craniata > Vertebrata > Gnathostomata > Teleostomi > Eutelostomi > Sarcopterygii > Dinotetrapodomorpha > Tetrapoda > Amniota > Mammalia > Theria > Eutheria > Boreoeutheria > Euarchontoglires > * > Primates> Haplorrhini > Simiiformes > Catarrhini > Hominoidea > Hominindae > * > Homininae > * > Homo

  • TFS says:

    The Christian Science Monitor reports on the newly announced Open Tree of Life, a freely accessible unified interface to, and archive, of biological taxonomies.

    A crucial comma is in totally the wrong place there. It should say:

    The Christian Science Monitor reports on the newly announced Open Tree of Life, a freely accessible unified interface to, and archive of, biological taxonomies.

  • Wikispecies? (Score:3)

    by aNonnyMouseCowered ( 2693969 ) on Sunday September 20, 2015 @07:29PM (#50563889)

    Isn't this already being done with Wikispecies.org (https://species.wikimedia.org/wiki/Main_Page)?

    Catch phrases: "The free species directory that anyone can edit." "Wikispecies is free, because life is in the public domain!"

  • UCMP [berkeley.edu] has an online exhibit [berkeley.edu] that I find to be more browsable and complete than the other sites I've tried.

  • Wonderful - now all the scientific feuding over whether Amborella is the basal angiosperm can spill over into wiki edit wars.

    (Amborella trichopoda is a New Caledonian flowering plant (angiosperm) with no close relatives. The deepest split in the angiosperm phylogeny may be Amborella splitting from everything else. Much ink and enmity has been spent on whether or not this is so. Here [tolweb.org] is a summary I found, although on a skim read I suspect it was written by a partisan.)

  • It is inevitable that some organism has inherited so much of its genome by reverse transcriptase etc as to muddy the question of exactly what it descended from. Then artificial species will start showing up and it alls gets even messier than it is now. I wonder if it could eventually have cycles.

    • Via infection or intentional quasi-sexual gene exchanges. Common in bacteria. Less common in metazoa. However genetists suspect a small fraction (1% to 8%) of the human genome was came through retrovirus infection. Soem from hundreds of millions of years ago. https://en.wikipedia.org/wiki/... [wikipedia.org] Messes up creating these genetic taxometries.

  • http://tolweb.org/ [tolweb.org]
    Is also a Tree Of Life project, but unlike OpenTree, it have pictures and descriptions and it also contains extinct species.
    For examples for Aves:
    https://tree.opentreeoflife.or... [opentreeoflife.org]
    http://tolweb.org/Aves [tolweb.org]

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