More Human Evolution Diagrams

I'm nearing the end of work on a review of the case for human evolution. I've uploaded some of the diagrams to my Flickr account before. Some of these were just updated and some new ones were added: see The Case for Human Evolution (Flickr set).

This is probably my favorite of the lot, showing the congruence between morphological/paleontological data (including radiometric dates) and genetic data (including molecular clocks):

(Click to see full size.)

Can you spot the single discrepancy? (No fair reading the caption on Flickr first.)


UPDATE: Revised some of the images, temporarily removed one.

What I Do For a Living, Part 312: Dr. Facilier's Parlour

I recently completed a new application. This one is a collection of three games associated with Disney's upcoming animated film, The Princess and the Frog. This one requires a Facebook account: Dr. Facilier's Parlour. (Dr. Facilier is the villain of the movie.)

This is my first completed project using certain technologies:

• Facebook API
• Spark components (Flex 4 beta)
• Code Igniter PHP framework

Also see the Shadow Shakedown game therein for an example of how DisplacementMapFilter can be useful. (I also got to do a tiny bit of character animation there.)

I have to say I was very pleased with all of these new technologies. In particular, the Spark component set is a huge improvement over the previous Halo components. Skinning components is so easy now it's hard to imagine that it was ever difficult. Adobe has acted on the "Favor composition to inheritance" maxim, and it has paid off. Also, props to Code Igniter, with its flexible tools and strong emphasis on the MVC pattern, for making PHP development (something I had all but sworn off) actually kind of fun.

Enjoy!

Glimpses of Stuff I've Been Working On

Two long-term projects of mine should see the light of day soon. Here are some previews (click to see full size):

(Why does everything I do lately involve directed, acyclic graphs?)

Online NEXUS File Viewer

It's been a month since my last post, but I have a very good reason for the hiatus. Namely, I was busy getting married to this woman (at the Los Angeles County Museum of Natural History) and going on our honeymoon (in Sydney, Australia).

Now that I'm back in California, time to get back to work on Names on Nodes! I've just put together a small demo of two key parts of its functionality: the reading of NEXUS files and the displaying of phylogenetic networks. Click here to see the NEXUS Viewer demo. This application opens NEXUS files and displays the trees in them as a combined phylogenetic network.

Things you need to know:

1. You must have a NEXUS file stored locally on your computer to use this.
2. That file should have a TREES section. (If not, the viewer should just display a list of operational taxonomic units.)
3. This could get messy for NEXUS files with lots of trees. (Although it's kind of neat-looking.)
4. You can move the nodes around by clicking on them, or click anywhere else to move the entire diagram.
5. I would dearly love to know if, for some reason, it does not work for a given file.

Enjoy!

Two "Names on Nodes"-Related Launches

I'm still a clear way away from launching the beta application, but I've just made a couple of launches related to my long-time work-in-progress, Names on Nodes.

First up, and probably of more interest to most people, I've begun the documentation for the MathML definitions used by Names on Nodes. The document includes general reviews of relevant mathematical and biological concepts, a quick review of MathML and the technologies it's based on, some comments on correlating mathematical and biological concepts, and definitions for all entities (including operations) used by Names on Nodes. Note that this covers a lot of the same ground as in my 2007 paper, with a few minor changes in the symbols and terminology (e.g., I now call the ancestor of a clade a "cladogen" rather than a "cladogenetic set").

Secondly, I've made the project open-source, by moving it to Google Code. If you are a developer interested in checking this out, go here. It's incomplete, so I don't know if anyone will have any real interest in looking at it yet. (Honestly, I mostly posted so that, on the off chance that I unexpectedly kick the bucket, my magnum opus won't be lost forever.)

This information is also on the new Names on Nodes home page.

"The Case for Human Evolution" - Illustrations

I have been working on an essay entitled The Case for Human Evolution for a while. I've just posted some illustrations I've been working on:

The Case for Human Evolution (Flickr Set)

Enjoy!

New Useless Utility: Text Tree Maker

I finally got around to launching something at namesonnodes.org. No, it's not Names on Nodes itself, unfortunately. The project is taking a huge amount of time. But I thought I'd post something, so here's a little Flex application I made (using the new Flash Builder 4 Beta!) using a smidgen of the technology behind Names on Nodes.

Have you ever been discussing phylogeny online and wished there was an easy way to make a readable cladogram? (95% of readers leave.) Those of you who are left, check this out: Text Tree Maker. Just type in a Newick tree string, and voilá! Okay, so typing in a Newick tree string is not that easy in the first place, but it is easier.

Well, I'll be using it, anyway. Check this one out!

Ardipithecus
|--ALA-VP 2/10
`--+--ARA-VP 6/1
   |--KNM-T1 13150
   `--Praeanthropus
      |--KNM-KP 29281
      `--+--AL 288-1
         |--KNM-WT 40000
         |--KT 12/H1
         |--LH 4
         `--+--BOU-VP 12/130
            |--Australopithecus
            |  |--Taung 1
            |  |--Australopithecus (Paranthropus)
            |  |  |--SK 6
            |  |  `--TM1517
            |  `--Australopithecus (Zinjanthropus)
            |     |--KNM-WT 17000
            |     |--OH 5
            |     `--Omo 18
            `--Homo
               |--KNM-ER 1470
               |--KNM-ER 1813
               |--OH 7
               |--OH 9
               `--Homo (Homo)
                  |--D 2600
                  |--KNM-ER 992
                  |--LB 1
                  `--+--Ceprano 1
                     |--Trinil 2
                     `--Homo (sapiens)
                        |--ATD 6-5
                        `--+--Mauer 1
                           `--+--Neandertal 1
                              `--+--Florisbad 1
                                 |--Kabwe 1
                                 `--Uppsala domkyrka: Carolus Linnaeus

NOTE: Right-click on the application and select "View Source" if you want to see some of the code behind it.