University of Glasgow

Roderic Page

Matt Yoder ([@mjyoder](http://twitter.com/mjyoder) had a Twitter
conversation yesterday about phylogeny viewers, prompted by my tweeting
about my latest displacement activity, a 2D tree browser using the
tiling approach made popular by Google Maps. 
 
As part of that conversation, [Matt
tweeted](http://twitter.com/mjyoder/status/40438156381794304): 

> RT @rdmpage: @mjyoder - I think 3D is the worse thing we could do,
> there\'s no natural mapping to 3D. \<- meh, where\'s the imagination?

 
Well, Matt\'s imagination has gone into overdrive, and he\'s [blogged
about his
ideas](http://cyphy.blogspot.com/2011/02/you-are-in-maze-of-twisty-little.html). 
 

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![3d_tree_browsing.jpg](http://lh4.ggpht.com/_Gct8lVAxKqQ/TWZCOrRP_iI/AAAAAAAAA18/vWgbdJNT0ec/3d_tree_browsing.jpg?imgmax=800){border="0"
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This issue deserves more exploration, but here are some quick thoughts.
3D has been used in a number of phylogeny browsers, such as Mike
Sanderson\'s
[Paloverde](http://loco.biosci.arizona.edu/paloverde/paloverde.html),
[Walrus](http://dx.doi.org/10.1186/1471-2105-5-48), and the [Wellcome
Trust\'s Tree of
Life](http://iphylo.blogspot.com/2009/02/thoughts-on-wellcome-interactive-tree.html).
I don\'t find any terribly successful, pretty as they may be. I think
there are several problems with trees in general, and 3D versions in
particular. 
 
**Trees aren\'t real** 
Trees aren\'t real in the same way that the physical world is (or even
imagined physical worlds). Trees are conceptual structures. The history
of web interfaces is littered with attempts to visualise conceptual
space, for example to summarise search results. These have been
failures, a simple top ten list as used by Google wins. I don\'t think
this is because Google\'s designers lack imagination, it\'s because it
works. Furthermore, this is actually a very successful visualisation: 
 

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I think elaborate attempts to depict conceptual spaces on screens are
mostly going to fail. 
 
**Trees are empty** 
Compared to, say, a geographic map, trees are largely empty space. In a
map every pixel counts, in that it potentially represents something.
Think of the satellite view in Google Maps. Each pixel on the screen has
information. Trees are largely empty, hence much of the display space is
wasted. Moving trees to 3D just gives us more space to waste. 
 
**Trees don\'t have a natural ordering** 
Even if we accept that trees are useful visualisations, they have
problems. Given the tree `((1,2),(3,4));` we have a lot of (perhaps too
much) freedom in how we can depict that tree. For example, both diagrams
below depict this tree. In the *x*-axis there is a partial order of
internal nodes (the ancestor of {1,2} must be to the right of the
ancestor {1,2,3,4}), but the tree `((1,2),(3,4));` says nothing about
the relative ordering of {1,2} versus {3,4}. We are free to choose. A
natural linear ordering would be divergence time, but estimates of those
times can be contested, or unavailable. 
 

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Phylogenies are *unordered trees* in the sense that I can rotate any
node about it\'s ancestor and still have the same tree (compare the two
trees above). Phylogenies are like mobiles: 
 

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aktiviere JavaScript, falls es in deinem Browser deaktiviert sein
sollte.
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The practical consequence of this is that different tree viewers can
render the same tree in very different ways, making navigation across
viewers unpredictable. Compare this to maps. Even if I use different
projections, the maps remain recognisably similar, and most maps retain
similar relationships between areas. If I look at a map of Glasgow and
move left I will end up in the Atlantic Ocean, no matter if I use Google
Maps or Microsoft Maps. Furthermore, trees grow in a way that maps
don\'t (at least, not much). If I add nodes to a tree it may radically
change shape, destroying navigation cues that I may have relied on
before. Typically maps change by the addition of layers, not by moving
bits around (paleogeographic maps excepted). 
 
**Trees aren\'t 3D** 
There\'s nothing intrinsically 3D about trees, which means any mapping
to 3D space is going to be arbitrary. Indeed, most 3D viewers simply
avoid any mapping and show a 2D tree in 3D space, which seems rather
pointless. 
 
Perhaps it\'s because I don\'t play computer games much (went through an
Angry Birds phase, and occasionally pick up an X-Box controller, only to
be mercilessly slaughtered by my son), but I\'m not inspired by the
analogy with computer games. I\'m not denying that there are useful
things to learn from games (I\'m sure the controls in Google Earth owe
something to games). But games also rely on a visceral connection with
the play, and an understanding of the visual vocabulary (how to unlock
treasure, etc.). Matt\'s 3D model requires users to learn a whole visual
vocabulary, much of which (e.g., \"Fruit on your tree? Someone has left
comment(s) or feedback. \") seems forced. 
 
My sense is that the most successful interfaces make the minimal demands
on users, don\'t fight their intuition, and don\'t force them to accept
a particular visualisation of their own cognitive space. 
 
I\'ll write more about this once I get my 2D tree viewer into shape
where it can be shown. It will be a lot less imaginative than Matt\'s
vision, all I\'m shooting for is that it is usable.

Matt Yoder (@mjyoder had a Twitter conversation yesterday about phylogeny viewers, prompted by my tweeting about my latest displacement activity, a 2D tree browser using the tiling approach made popular by Google Maps.As part of that conversation, Matt tweeted:Well, Matt's imagination has gone into overdrive, and he's blogged about his ideas. This issue deserves more exploration, but here are some quick thoughts.

Why 3D phylogeny viewers don't work

It\'s Friday, so time for some random, half-baked ideas. Imagine that we
have a database of evolutionary trees, and these overlap for a set of
taxa that we are interested in. How do we summarise these trees? One
approach is to make a supertree. It would be useful to display the
subtrees that went into making this supertree, if only to give an idea
of how much they agree with the supertree. How to do this?  
  
One idea I\'ve been toying with is inspired by
[Photosynth](http://photosynth.net/), from Microsoft labs (it only runs
on Windows, sigh). Photosynth takes a series of pictures taken from
different angles and stiches them together into a 3D model of the object
being photographed:  
[![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhxWLOJPdq1LhnlXbHjzyEPnEw5OZmemgREQoLN_mSb2Ly70pZRTAFTH_YeC9b-aBItaFqFIpB8ZQ0Jph1HfZUoep88I5ExnccodaWz2h_odui7QchiFxNp5JR1Zpw4U3DS2LnG/s400/photosynth.jpg){#BLOGGER_PHOTO_ID_5310027871757899586
style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 305px;"
border="0"}](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhxWLOJPdq1LhnlXbHjzyEPnEw5OZmemgREQoLN_mSb2Ly70pZRTAFTH_YeC9b-aBItaFqFIpB8ZQ0Jph1HfZUoep88I5ExnccodaWz2h_odui7QchiFxNp5JR1Zpw4U3DS2LnG/s1600-h/photosynth.jpg){onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"}  
  
One thing I like about Photosynth is that you can see the original
pictures, so when you move around the view you get a sense of how they
have contributed to the overall view. This is easier to see than
explain:  
  

  
  
Now, imagine if we did this with trees. We could create a supertree as a
summary of the individual trees, then have the original trees layered on
top. Perhaps we could do this in 3D, so that each individual tree is in
a plane that is tilted with respect to the supertree in proportion to
how much it disagrees with the supertree:  
[![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiPUmF4U1QCR9blIBLdefVl1byxQ5teQHB3zVEtwZyE6doK5BM_XZ4kKHrFe2AKuOVx01YSlrXZDzDdGDZ4p5ihN3ppcT4Bb6xoIzq185nnwAyM_DtTUJ5A3ZNshpH6BSoipExi/s400/phototree.jpg){#BLOGGER_PHOTO_ID_5310032549276503842
style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 352px; height: 154px;"
border="0"}](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiPUmF4U1QCR9blIBLdefVl1byxQ5teQHB3zVEtwZyE6doK5BM_XZ4kKHrFe2AKuOVx01YSlrXZDzDdGDZ4p5ihN3ppcT4Bb6xoIzq185nnwAyM_DtTUJ5A3ZNshpH6BSoipExi/s1600-h/phototree.jpg){onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"}  
I think this could be a fun way to explore a set of trees, and it would
give one the ability to quickly grasp how well the source trees agreed
with the supertree. Note that I\'m not (necessarily) arguing that the
supertree represents the try phylogeny. Think of it as a convenient way
to summarise the individual trees.  
  
Part of what attracts me to this approach is that I think most, if not
all, 3D phylogeny viewers (such as
[Paloverde](http://loco.biosci.arizona.edu/paloverde/paloverde.html) and
the [Wellcome tree of
life](http://iphylo.blogspot.com/2009/02/thoughts-on-wellcome-interactive-tree.html))
don\'t make any real use of 3D, beyond the rather gimmicky (and I find
ultimately confusing) ability to fly around a 2D tree. Is there a better
way to exploit the possibilities of 3D?


It's Friday, so time for some random, half-baked ideas. Imagine that we have a database of evolutionary trees, and these overlap for a set of taxa that we are interested in. How do we summarise these trees? One approach is to make a supertree. It would be useful to display the subtrees that went into making this supertree, if only to give an idea of how much they agree with the supertree.

Photosynth for trees - supertrees revisited

Really just a shameless attempt to get one over [David
Shorthouse](http://ispiders.blogspot.com), but there has been
[some](http://blogs.nature.com/news/thegreatbeyond/2007/10/52m_year_old_spider_xray.html)
[buzz](http://news.bbc.co.uk/1/hi/sci/tech/7068160.stm) about Very High
Resolution X-Ray Computed Tomography (VHR-CT) of a fossil of
*Cenotextricella simon*.  
  
[![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjPnjAhbjH7ZR0jxRyFBJ3BIeu5aReCHPad4kSFomdGhJ2tax49nBYZz9IfDJ_N9K_8UqH8GIKm8gj0jCGAg3m4H28PWSEaJ_6baP3sUM-55Qiqt_m4y2_IaLNvQw2aOGhKETzf/s320/spider.jpg){#BLOGGER_PHOTO_ID_5127405251510902594
style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;"
border="0"}](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjPnjAhbjH7ZR0jxRyFBJ3BIeu5aReCHPad4kSFomdGhJ2tax49nBYZz9IfDJ_N9K_8UqH8GIKm8gj0jCGAg3m4H28PWSEaJ_6baP3sUM-55Qiqt_m4y2_IaLNvQw2aOGhKETzf/s1600-h/spider.jpg){onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"}  
The paper describing the work is in *Zootaxa* (link
[here](http://www.mapress.com/zootaxa/2007f/z01623p053f.pdf)). *Zootaxa*
is doing great things for taxonomic publishing, but they really need to
get some sort of stable identifier set up. Linking to *ZooTaxa* articles
is not straightforward. If they had DOIs (or even OpenURL access) they
wuld make it much easier for people to convert lists of papers that
include *ZooTaxa* publications to lists of resolvable links.


Really just a shameless attempt to get one over David Shorthouse, but there has been some buzz about Very High Resolution X-Ray Computed Tomography (VHR-CT) of a fossil of

 Cenotextricella simon

.The paper describing the work is in

 Zootaxa

(link here).

 Zootaxa

is doing great things for taxonomic publishing, but they really need to get some sort of stable identifier set up. Linking to

 ZooTaxa

articles is not

Amber spider

[![](https://www.nescent.org/wg/EvoViz/images/f/f1/Hylidae_allpolygons.png){style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 320px;"
border="0"}](https://www.nescent.org/wg/EvoViz/images/f/f1/Hylidae_allpolygons.png)  
David Kidd has put together [evoviz.org](http://evoviz.org/). To quote
from the wiki:  

> EvoViz is a collaborative Wiki space within which scientists,
> educators and artists can present and discuss the visualization of
> evolutionary concepts, processes and data.

  
There is movie demo online at
[GUBA](http://www.guba.com/watch/3000037924).


David Kidd has put together evoviz.org. To quote from the wiki:There is movie demo online at GUBA.

Publicaciones de Rogue Scholar

Why 3D phylogeny viewers don't work

Photosynth for trees - supertrees revisited

Amber spider

EvoViz