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A Wikipedia-Style Tree of Life Emerges

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.

12 of 72 comments (clear)

  1. Kardashian? by chill · · Score: 3, Funny

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

    --
    Learning HOW to think is more important than learning WHAT to think.
    1. Re:Kardashian? by Darinbob · · Score: 2

      Yes we all know she is burdened with a big ass. Which is why you should never rush into a marriage.

  2. Almost Cool by JMJimmy · · Score: 3, Interesting

    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.

  3. Now it just needs complete genome sequences... by NicknameUnavailable · · Score: 2

    ...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.

  4. Re:Very Cool by fluffernutter · · Score: 2

    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.

    --
    Laws are rules for the court, but merely a bottom bar to hit for life. Think beyond laws in your actions always.
  5. The Tree of Life can't Handle Open Source by tinkerton · · Score: 2

    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.

  6. graphical Harvard museum effort not available by call+-151 · · Score: 2

    It's really too bad that the fabulous museum exhibit display Deep Tree 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 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 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 psychosomatic. You need a lobotomy. I'll get a saw.
    1. Re:graphical Harvard museum effort not available by Michael+Woodhams · · Score: 2

      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 chicken, you can walk it: start at H. sapiens, walk back to the mammal/dinosaur common ancestor, then forwards taking the correct paths until you reach G. gallus. The dinosaur part of the museum will be 65+ meters from the main part of the museum (representing the current day.) The main grounds of the museum will be about 550m long to cover Cambrian explosion to current day. About 3.5km away will be a much smaller museum about the origin of life. Somewhere in between will be a small museum about the origin of eukaryotes. At selected branching points on the phylogeny there will be metal cubes beside each branch, the volume of which are proportional to the now-living biomass descended from each branch.

      There are some practical challenges in building this museum that I haven't worked out. Should I find myself with a few hundred million dollars and nothing better to spend them on, I'll give those challenges serious thought. (Or pay someone else to give them serious thought.)

      --
      Quattuor res in hoc mundo sanctae sunt: libri, liberi, libertas et liberalitas.
  7. Re:Christian Science Monitor by TapeCutter · · Score: 4, Insightful

    I have been atheist/agnostic for over 50yrs, CSM has been in print for 100. In my experience CSM understands (and chronicles) science better than most MSM rags. Unlike Isaac Newton, I have never heard them spewing religious nonsense at their audience.

    --
    And did you exchange a walk on part in the war for a lead role in a cage? - Pink Floyd.
  8. Wikispecies? by aNonnyMouseCowered · · Score: 2

    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!"

  9. Re:Christian Science Monitor by quenda · · Score: 3, Informative

    This should have been in the summary. For those who don't know:

    - Christian Science as a religion has strong anti-science beliefs, including rejection of modern medicine in favour of prayer. BUT ...

    - The CSM newspaper is a highly respected news source, mostly independent from the religion except for a daily editorial. Think of it as being sponsored by the church.
        It has won seven Pulitzer Prizes.

  10. Re:Christian Science Monitor by quenda · · Score: 2

    I have been atheist/agnostic for over 50yrs, ... Unlike Isaac Newton, I have never heard them spewing religious nonsense at their audience.

    So for about 90% of your life so far, you were religious?