News Tree of life

Tree of life morphs into … leaf?

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new and expanded tree of life/Zosia Rostomian, Lawrence Berkeley

From ScienceDaily:

Scientists have dramatically expanded the tree of life, which depicts the variety and evolution of life on Earth, to account for thousands of new microscopic life forms discovered over the past 15 years. The expanded view finally gives bacteria and Archaea their due, showing that about two-thirds of all diversity on Earth is bacterial — half bacteria that cannot be isolated and grown in the lab — while nearly one-third is Archaeal.

This is great but no way is it a tree. Readers, what would you call it?

One striking aspect of the new tree of life is that a group of bacteria described as the “candidate phyla radiation” forms a very major branch. Only recognized recently, and seemingly comprised only of bacteria with symbiotic lifestyles, the candidate phyla radiation now appears to contain around half of all bacterial evolutionary diversity.

While the relationship between Archaea and eukaryotes remains uncertain, it’s clear that “this new rendering of the tree offers a new perspective on the history of life,” Banfield said. Paper. (public access) More.

The relationship between the Archaea and eukaryotes is in fact so uncertain that prominent figures such as the late Carl Woese and Craig Venter doubt they have a common origin. Presumably, it would be just as easy (or difficult) to account for their existence without a common origin.

In the present state of uncertainty, we surely can’t rule out an orchard of life.

23 Replies to “Tree of life morphs into … leaf?

  1. 1
    wd400 says:

    This is great but no way is it a tree. Readers, what would you call it?

    A tree. Because that’s what it is. How it is illustrated makes no difference.

  2. 2
    News says:

    wd400, why don’t we call it a tomcat then?

    It is very narrow at one point. Do we know that that point even exists? Or is that just assumed?

    Added: There used to be one that looked like a kumbayah circle. That was coulpe seasons ago though.

  3. 3
    Zachriel says:

    The full tree inference required 3,840 computational hours on the CIPRES supercomputer.

    Here’s the close-up view of the tree:
    http://www.nature.com/articles...../figures/1

  4. 4
    Zachriel says:

    News: There used to be one that looked like a kumbayah circle.

    It’s still a mathematical tree.

    “a tree is an undirected graph in which any two vertices are connected by exactly one path.”
    https://en.wikipedia.org/wiki/Tree_(graph_theory)

    The branches of an oak form a mathematical tree, as does this:
    http://www.zo.utexas.edu/facul.....fLife2.jpg


    Edited for clarity.

  5. 5
    REW says:

    News
    Why the hostility to referring to it as a tree?

  6. 6
    News says:

    REW at 5: It’s not hostility. But this thing is not a tree. It’s nice but shouldn’t be called a tree.

    Wen the idea was first developed, we thought about life differently and the term made sense.

    I see a kite, actually.

  7. 7
    earthsinterface says:

    I see one of those mythological Chinese New Years Dragons

  8. 8
    wd400 says:

    News. It’s a tree. That you don’t know what a tree is is really your own problem.

  9. 9
    earthsinterface says:

    wd40
    “News. It’s a tree. That you don’t know what a tree is is really your own problem.”

    Ah yes, I see said the blind Man to his deaf Son, it’s a piece of seaweed branch

  10. 10
    Rob says:

    I see the Archaeopteryx…how ironic!

  11. 11
    daveS says:

    This is great but no way is it a tree. Readers, what would you call it?

    Definitely not a tree. Looks like a Leafy Sea Dragon to me.

  12. 12
    earthsinterface says:

    DaveS

    Definitely not a tree. Looks like a Leafy Sea Dragon to me.

    Hey that was my third choice as well and I think the best

    http://sites.psu.edu/chenedrcl.....dragon.jpg

  13. 13
    Dionisio says:

    REW @5

    Glad you’re back.
    Would you have time to answer the questions @15 in the discussion thread pointed by the following link?

    http://www.uncommondescent.com.....ent-601952

    Thanks.

  14. 14
    REW says:

    News
    Well of course its not literally a tree but it has the same bifurcating branching pattern as a tree ( ignoring horizontal gene transfer)

    Dave
    Yes! It does look like that actually!

    Dionisio
    Sure. I can see he does the breath between topics. I know it relieves stress but I’m doubtful it would in a classroom situation like that…..or were you referring to my comment on the James Tour video?

  15. 15
    Mung says:

    Looks like a Leafy Sea Dragon to me.

    But a Leafy Sea Dragon is a tree.

  16. 16
    Mung says:

    I don’t mind calling it a tree for the same reason I don’t mind calling the genetic code a code.

    I also think the usual scare quotes around the word code are about as useful as putting scare quotes around the word tree.

  17. 17
    Zachriel says:

    Mung: I also think the usual scare quotes around the word code are about as useful as putting scare quotes around the word tree.

    In mathematics, ‘tree’ has a precise definition that applies to the branching shown in “A new view of the tree of life”, as well as to the branching in a oak tree. The problem with the word ‘code’ is that, in these sorts of discussions, it is rarely well-defined.

  18. 18
    Andre says:

    News

    I think there is an easier explanation; the paper states

    Charles Darwin first sketched a tree of life in 1837 as he sought ways of showing how plants, animals and bacteria are related to one another.

    God forbid that Darwin is even more wrong, if this nonsense is ultimately shown as wrong (which has been of late) the Darwinian apostle’s entire world would collapse, again God forbid…..

    What Darwin got wrong so far and more follows everyday…..

    http://www.amazon.com/What-Dar.....031268066X

    And I am happy to stand my ground on this, there is no other reason, you see simple minded people get bamboozled by fairy stories quite easily, just look at the same crowd that believe Darwin also believe that man is the cause of climate change. the also believe that mud not only made itself but magically became alive. They are also the same crowd that believe objective morals don’t exist and by a large amount, their biggest flaw, there is no God. They are most welcome to prove me wrong…. They know better, or maybe not…

  19. 19
    Bob O'H says:

    I reckon you’re all looking at the details too much. It’s actually a wood.

  20. 20
    daveS says:

    Hmm.

    From the article: “Figure 2: A reformatted view of the tree in Fig. 1 [the leaf pictured in the OP] which each major lineage represents the same amount of evolutionary distance.”

    Here’s a jpg of Figure 2. That looks more tree-like.

    Edit: The leaf/tree is freely available in Newick tree format here, so I guess there’s actually no doubt it is in fact a tree (notwithstanding its various pictorial representations).

  21. 21
    Mung says:

    Zachriel: The problem with the word ‘code’ is that, in these sorts of discussions, it is rarely well-defined.

    And you think putting scare quotes around the word helps?

  22. 22
    Zachriel says:

    Mung: And you think putting scare quotes around the word helps?

    As long as the meaning of “tree” and “code” is clearly understood, there’s no reason to use scare-quotes. The former is not subject to conflation. No one thinks the phylogenetic tree is a plant. As to the latter, there are several related definitions that are often conflated.

  23. 23

    Tree or leaf, consider this:

    “This is humbling,” says Jonathan Eisen from the University of California, Davis, “because holy **#$@#!, we know virtually nothing right now about the biology of most of the tree of life.”

    http://www.theatlantic.com/sci.....er/477729/

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