Flex Builder 3 Deep Linking: Awesome!

O.K, so, a little history.

Everyone reading this is aware of what a website is. Generally, it's a collection of hypertext pages that cross-link to each other.

At least, that's what they used to be. Increasingly over the past decade, more and more Flash websites have appeared. A Flash website is generally one interactive "movie" file that dynamically loads content according to user actions. In other words, a Flash website is not a collection of "pages"—it's a (potentially) complex application that can take on many different states.

With a traditional hypertext website, linking to any particular "page" is simple. Even linking to particular sections of particular pages is simple. Each page has its own address (a URL—Uniform Resource Locator), so you can just grab that in your browser and pass it off to someone else.

With Flash websites, it becomes a lot more complicated. The state of the Flash movie is not automatically reflected in the URL. Generally, you have to implement some kind of complex system, using JavaScript, to tack on information to the URL. The information flow has to go both ways. Flash has to be able to read the URL, determine the proper state, and move into it. At the same time, whenever the user induces Flash into entering a different state, that must be reported to the browser so it can be reflected in the URL. It's a major pain.

Enter Flex Builder 3.

Flex Builder is a development tool (also available as a plugin for the Eclipse development platform, which is what I use) that generates Flash content. Not long ago, Adobe released an alpha version of version 3.

I had heard that they had added a deep-linking feature, and had been meaning to read up on it Doubtless they would it some kind of customized implementation with my components.

Wrong.

Last night I was troubleshooting a bug with March of Man, and happened to upload some files generated by Flex Builder 3, which had not previously been uploaded. All of a sudden, there it was: deep-linking to every major section of the site.

I barely had to lift a finger.

Regard:

• F.A.Q.
• Field Guide
• Image Gallery
• Collage
  

O.K., so it's not perfect. The URLs are a bit ugly, and I'm not sure if they're going to work with future versions of the website. Also, it'd be nice if the browser title changed. But I'm sure with a little delving into the documentation and a few tweaks, it should be possible.

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On another note, I am no longer the only artist on March of Man! (Well, already some of my works are heavily based on photographs taken by others, which is why I need to implement multiple attributions, but anyway....) With the addition of Stephen O'Connor's Homo erectus, this is finally what it was meant to be: a collaborative paleo-art project.

March of Man Skewed

Posted a very minor March of Man update last night. Now the collages can be horizontally skewed. Examples (click to enlarge):

(Vertical distribution primarily based on phylogeny.)

(Vertical distribution based on geography.)

(You'll note I also finished some more Homo sapiens sapiens depictions.)

New: March of Man Collages

I've just uploaded a new version of March of Man. The primary new feature is a tab called "Collage", which contains a first attempt at the doing what the project is all about: creating an image that uses multiple figures to show to story of hominin phylogeny and geographic dispersal.

An auto-generated March of Man collage.

Okay, so there's still a lot to be done. There are only 13 images in the database so far (all mine, although some are heavily based on others' photos), so there are plenty of gaps to fill in.

Collage features planned for the future:

• Better backgrounds.
• Different algorithms for generating the collages. (This will only become important once the database has many, many more images.)
  
• The ability to move, rotate, and scale images in the collage.
• The ability to add filters to images (adjusting the color, contrast, etc.).
• The ability to save collages.

(I'd also like to figure out a way to have it spit out PSD files, but since that's not an open format....)

As I further refine this tool, and as the database of images continues to grow, the collages will become more and more like I first envisioned. (Or maybe some other ideas will become apparent later on ... this isn't a rigorously planned-out project.)

Some other things I intend to add to the site:

• The ability to attribute more than one artist per image.
• "Starter" PSD files that can be downloaded, including tiled isometric backgrounds and scale indications.
• A scale widget that's easier to use.
• Illustrated instructions for exporting the right kind of file.
• An administration tool, so I can update data on the various taxa more readily.
• More illustrations (and better ones) for the "About" and "F.A.Q." sections.
• Thumbnail images for browsing.

That should keep me plenty busy for a while. Anyone have any other ideas?

Qayin wa-Habel
(Cain and Abel)
Ardipithecus ramidus juveniles

Trees, Bubbles, and Hooves

"Bubble-Thinking"

Over the past few decades, there has been a major shift in how scientists think about organism relationships at larger scales. Open up a textbook on evolution and you will probably see what's referred to as a "bubble diagram". Over the ages, it will show various groups swelling in size and then tapering off, but often spitting off one or more other such "bubbles" before they completely die out. Here's an example:

If your textbook has a diagram like this, you may need a new textbook.

This shows the evolution of hoofed mammals since the end of the Cretaceous (about 65 million years ago). A generalized bunch of mammals called "Condylarthra" spits off several radiations before it goes extinct: Artiodactyla (even-toed ungulates: pigs, hippos, camels, ruminants, etc.), Perissodactyla (odd-toed ungulates: horses, rhinos, tapirs, etc.), Tubulidentata (aardvarks), Hyracoidea (the superficially rodent-like hyraxes), Proboscidea (elephants, etc.), Sirenia (manatees, dugongs, etc.), and some extinct groups like Desmostylia and a large South American group. At least one of these radiations, Artiodactyla, spits off its own new radiation: Cetacea, the whales.

This diagram nicely shows population changes over time and is pretty instantly comprehensible. Unfortunately, it's also wrong, WRONG, WRONG.

First of all, it obscures the actual relationships of the "parent taxon" to the "daughter taxon". Obviously, some "condylarths" will be closer to one or more of the "daughter taxa" than they are to other condylarths. Why lump them in with organisms they share less common ancestry with? The group "Condylarthra" is simply unnatural. "Artiodactyla", as shown here, is unnatural, too—hippos are probably closer to cetaceans than they are to other artiodactyls.

Furthermore, recent molecular studies have shown that "Ungulata" is not a natural group. Some of these lineages—Hyracoidea, Proboscidea, Sirenia, and Tubulidentata—are part of Afrotheria, an endemic African clade including golden moles, tenrecs, otter shrews, elephant shrews (sengis), etc. Perissodactyla is allied to Ferae (carnivorans and pangolins), and Artiodactyla is allied to a group including Chiroptera (bats), Ferae, and Perissodactyla, which was rather creatively named Pegasoferae ("Pegasus wild beasts").

(As for the extinct South American ungulates, obviously molecular studies aren't going to tell us much, and I don't think anyone's done the morphological legwork yet—if anyone can knows of such a study, please enlighten me.)

In short, "ungulates" are not a phylogenetic group, but more of a general ecological form, one which several placental lineages arrived at independently (and some, like cetaceans and sirenians, secondarily lost as they became aquatic). There is no such thing as one "origin of the ungulates"—there were many such origins.

"Tree-Thinking"

Under newer paradigms, we don't think of higher taxa as bubbles that spit off other bubbles. Instead, higher taxa are clades: an ancestor and all of its descendants. Artiodactyla did not spit off Cetacea; instead, Artiodactyla includes Cetacea.

Placentalia
|--Atlantogenata
|  |--Xenarthra (sloths, armadillos, anteaters)
|  `--Afrotheria
|     |--Afroinsectiphilia
|     |  |--Macroscelididae (elephant shrews)
|     |  `--+--Orycteropus afer (aardvark) *
|     |     `--Afrosoricida (golden moles, tenrecs, etc.)
|     `--Paenungulata *
|        |--Elephantidae *
|        `--+--Procaviidae (hyraxes) *
|           `--Sirenia *
`--Boreotheria
   |--Supraprimates
   |  |--Glires (rodents, rabbits, etc.)
   |  `--Euarchonta (primates, etc.)
   `--Laurasiatheria
      |--Eulipotyphla (shrews, moles, hedgehogs, etc.)
      `--Scrotifera
         |--Artiodactyla *
         |  |--Camelidae (camels, llamas) *
         |  `--+--Suoidea (pigs, peccaries) *
         |     `--+--Ruminantia (deer, antelope, etc.) *
         |        `--Whippomorpha *
         |           |--Cetacea *
         |           `--Hippopotamidae *
         `--Pegasoferae
            |--Chiroptera
            `--Zooamata
               |--Perissodactyla *
               `--Ferae
                  |--Carnivora (dogs, cats, etc.)
                  `--Manis(pangolins)

* hoofed or ancestrally hoofed

Cladogram showing the distribution of hooves among extant placental mammals. Some of the particulars remain under debate, but the picture is becoming clearer.

What about the condylarths? Work is still going on to see how these fit into the newer ideas about placentalian phylogeny. They are probably an unnatural group with multiple origins. One recent study suggests that some may not even belong to the crown group—they may be stem-placentals, on one or more side-branches to Placentalia.

So What?

Understanding phylogeny is crucial to investigating questions about the history of life. For example: what caused the mass extinctions at the end of the Cretaceous? This is a question which has received a lot of attention, both scientific and popular.

To even begin to answer this question, we have to know which groups of organisms perished and which made it through. Specifically, many researchers are curious as to whether a given diverse crown group started to diversify before the extinction, or survived as a single lineage which diversified afterwards. As an example, there is evidence to suggest that the crown group of birds had started to diversify earlier, with at least six lineages surviving into the Cenozoic (the current era).

Obviously, one such group of interest is Placentalia (all researchers being lifelong members). Did a single lineage squeak through (ha ha!) by the hair on its chin (my sides!) to give rise to atlantogenates and boreotheres later, or had placental mammals already begun to diversify before the mass extinctions began, at the feet of the dinosaurs?

The Kharmer "Ungulate"

Earlier this month (a day before my birthday, in fact), a paper was published which tentatively suggests the latter case: placentals diversified before the extinction. Titled A Cretaceous Hoofed Mammal from India, it names a new species, Kharmerungulatum vanvaleni, based on a single lower molar. As this molar shows similarities to those of Protungulatum, an early condylarth, K. vanvaleri is assigned to Condylarthra. The authors suggest that this may mean that the ancestors of ungulates had diversified before the end of the Cretaceous, perhaps especially in Gondwana.

To me this is a clear example of the dangers of "bubble-thinking". Phylogenetic research has shown us that "ungulates" are not an evolutionary unit. Hence, the "ancestors of ungulates" are really "ancestors of placentals". Furthermore, it may be that Protungulatum is part of a side-branch to the placentals, so if this new Indian taxon is closely related to Protungulatum (and even that evidence is scanty), then it may not even be a placental. All this tooth really tells us is that some therian lived in India toward the end of the Cretaceous. And that has no bearing at all on the question of whether placentals originated during or after the Cretaceous.

However, if Kharmerungulatum does share a clade with Protungulatum to the exclusion of placentals, then it would be part of another clade that persisted across the boundary, but died out soon thereafter. Why did this clade and the ancestors of placentals survive? Why did placentals win out in the aftermath? Perhaps this new taxon can help us answer these types of questions, which come from a "tree-thinking" perspective. Of course, so far, Kharmerungulatum is just a tooth—but maybe more material is out there.

Phylogeny diagram showing major placental groups and some "condylarths", including a tentative position for the new taxon. The Cretaceous/Paleogene extinction occurred at the color boundary, about 65 million years ago.

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References

• Beck, R. M. D., O. R. P. Bininda-Emonds, M. Cardillo, F.-G. R. Liu, and A. Purvis (2007 Nov. 13). A higher-level MRP supertree of placental mammals. BMC Evolutionary Biology 6(93). doi:10.1186/1471-2148-6-93
• Clarke, J. A., C. P. Tambussi, J. I. Noriega, G. M. Erickson, and R. A. Ketcham (2005 Jan. 20). Definitive fossil evidence for the extant avian radiation in the Cretaceous. Nature 433: 305-308. doi:10.1038/nature03150
• Hallström, B. M., M. Kullberg, M. A. Nilsson, and A. Janke (2007). Phylogenomic data analyses provide evidence that Xenarthra and Afrotheria are sister groups. Molecular Biology and Evolution 24(9): 2059-2068. doi:10.1093/molbev/msm136
  
• Nishihara, H., M. Hasegawa, and N. Okada (2006 June 27). Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions. Proceedings of the National Academy of Sciences 103: 9929-9934. doi:10.1073/pnas.0603797103
  
• Prasad, G. R., O. Verma, A. Sahmi, V. Parmar, and A Khosta (2007 Nov. 9). A Cretaceous hoofed mammal from India. Science 38: 937. doi: 10.1126/science.1149267
• Wible, J. R., G. W. Rougier, M. J. Novacek, and R.J. Asher (2007 June 21). Cretaceous eutherians and Laurasian origin for placental mammals near the K/T boundary. Nature 447: 1003-1006. doi:10.1038/nature05854

Who Ate What Now?

Most fossils, especially the older ones, are annoyingly incomplete. They'll find a few bones, or some footprints, a smudgy outline, etc. Then there are the more-or-less complete specimens, which are rarer but still not infrequent. And finally there are real "snapshots of life" which come along once in a great while. This latest discovery, for example:

Shark Ate Amphibian Ate Fish: First "Food-Chain Fossil"

Specimens with the remains of ingested animals are sometimes found, but I've never heard of this kind of "Russian doll" fossil before. Truly remarkable.

[image of the fossil, with reconstructions]

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And now that I've finished marveling at it, it's time for me to return to character and bemoan the nomenclatural inaccuracies!

First, what are the actual animals involved? It's an Acanthodes bronni, eaten by a temnospondyl, eaten by a Triodus sessili. Is the headline accurate? Let's establish a few ground rules first.

Most taxa (at least of those that have been around a while) are based on living organisms. When related fossil organisms are found, there is often some dispute as to whether to include them or not. For example, when Archaeopteryx was discovered, people couldn't decide if it was a bird or not. It had feathered wings and bird-like feet, but also had teeth and a long tail. Did it fly? Who knows.

In the past, some people have recommended letting taxa extend as far as possible, encompassing what is known as the total group. A total group includes everything sharing closer ancestry with the living members of a group than with any other living organisms. This approach can run into some serious problems, though. For example, it would make all dinosaurs birds. More generally, it lumps the earliest, barely differentiated members of a lineage in with their derived, living descendants. This encourages the use of unjustified inferences. For example, I know that all living birds have tertial feathers (long feathers along the upper arm), so, since Archaeopteryx is a bird, it should have them, too, right? WRONG. Analysis of the available fossils has yet to indicate the presence of any tertials.

This is why many others encourage the use of crown groups for common taxonomic names. A crown group is the final common ancestor of certain living organisms, and all descendants of that ancestor. Using a crown group definition for Aves, for example, would limit it to the clade of modern birds, thereby excluding Archaeopteryx. This practice has the effect of discouraging unjustified inferences.

One other term to note here is stem group. This is simply a total group minus its included crown group. For example, a stem-avian is anything sharing closer ancestry with birds than with other living organisms (e.g., crocodylians), but outside the crown group Aves. Archaeopteryx and all the classic dinosaurs are stem-avians, as are (probably) pterosaurs.

Archosauria
|-Pan-Crocodylia (including Crocodylia)
`-Pan-Aves
  |-Pterosauria *
  `-+-Marasuchus *
    `-+-Silesaurus *
      `-Dinosauria *
        |-Ornithischia *
        `-+-Herrerasauridae *
          `-+-Sauropodomorpha *
            `-+-Eoraptor *
              `-+-Coelophysoidea *
                `-+-Dilophosauridae *
                  `-+-Ceratosauria *
                    `-Tetanurae

Tetanurae
|-Spinosauroidea *
`-+-Carnosauria *
 `-+-Compsognathidae *
   |-Tyrannosauroidea *
   `-+-Ornithomimosauria *
     `-+-Oviraptoriformes *
       `-+-Deinonychosauria *
         `-+-Archaeopterygidae *
           `-+-Confuciusornithidae *
             `-+-Enantiornithes *
               `-+-Hesperornithes *
                 `-+-Ichthyornithes *
                   `-Aves

* extinct stem-avian taxon

Cladograms (somewhat abridged) showing the avian stem group.

Is Acanthodes a fish? Well, yes, they got that right. "Fish" is a really, really broad category, tantamount to "any craniate that isn't a tetrapod" (more or less). Specifically it is an acanthodian, which makes it a stem-osteichthyan (Osteichthyes being the crown group that includes bony vertebrates, e.g., ray-finned fishes, lungfishes, coelacanths, and tetrapods).

Are temnospondyls amphibians? O.K., this is harder. Traditionally, Amphibia was used as a "wastebasket taxon" for any tetrapod that was not an amniote. More recently, it has been limited to one of two groups: the total group including frogs, salamanders, and caecilians; or the crown group including frogs, salamanders, and caecilians. There is actually quite a bit of debate on this matter and I don't expect it to be resolved any time soon. According to the crown group usage, temnospondyls are definitely not amphibians. But according to the total group usage, they might be. (But they might also be stem-tetrapods or stem-amniotes.)

Is Triodus a shark? "Shark" is a really abused term in paleontology. (In fact, acanthodians are sometimes called "spiny sharks" even though they're not even chondrichthyans.) Among modern animals, the term is generally limited to Selachii, the flatter members of which are called skates or rays. Triodus is a stem-selachian, closer to sharks, rays, and skates than to ratfishes (Holocephali). So is it a shark? If we want to limit unjustified inferences, then we should say no.

Gnathostomata (jawed vertebrates)
|--Chondrichthyes (cartilaginous fishes)
|  |--Holocephali (ratfishes)
|  `--+--Triodus *
|     `--Selachii (sharks, rays, skates)
`--+--Acanthodes *
   `--Osteichthyes (bony vertebrates)
      |--Actinopterygii (ray-finned fishes)
      `--Sarcopterygii (flesh-finned vertebrates)
         |--Dipnoi (lungfishes)
         |--Latimeria (Recent coelacanths)
         `--Apo-Tetrapoda (limbed vertebrates)
            |?-Temnospondyli *
            `--Tetrapoda
               |--+?-Temnospondyli *
               |  `--Amniota
               `--Amphibia sensu lato
                  |?-Temnospondyli *
                  `--Amphibia sensu stricto

* extinct

Cladogram of the taxa in question, with related extant taxa.

Okay, smarty, how would YOU dumb this down? Argh, that's pretty hard. Personally I think the lay public might be ready for the term "stem-", but I seem to have a bad habit of overestimating the lay public. Anyway, the best I can come up with is "Stem-Shark Ate Limbed Creature Ate Fish." Doesn't roll off the tongue, you say? Well, I guess this is why I'm not a journalist....

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(References to be added later, if I have time.)

The Ten Commandments

From time to time I may post things I've written elsewhere, just to aggregate them under this new blog.

A couple of years ago I decided to try my hand at translating the Ten Commandments (from the Torah). Of course, there are three or four different versions. (The "or four" is because of one section that lists commandments, but more than ten.) The version people usually think of is probably a latter-day revision, presented in slightly different forms in two different parts of the Torah. But I was more interested in what is probably the oldest version.

And he [Yahweh] said, "So, I will cut a deal, making before all your kinsfolk exceptional things which were not created in all the land and in all the [lands of the] Goyim¹, and all the kinsmen who are among you will see the deeds of Yahweh², for it is a fearful thing which I will make your kinsfolk. Keep that which I command you this day. Lo, I will expel from before you the 'Emori³ and the Kana´ani⁴ and the Khiti⁵ and the Parizi⁶ and the Khiwi⁷ and the Yebusi⁸.

"[1] And keep yourselves, lest you cut a deal with dwellers of the land which you enter over, lest it turn to be a trap in your midst. For you are to pull down their sacrificial altars and break down their pillars and cut down their 'Asherah⁹ poles. For you are not to bow down to any other god¹⁰, for Yahweh the Jealous is his name; a jealous god he is; lest you cut a deal with dwellers of the land, and they whore themselves to their other Gods, and sacrifice to their Gods, and call to you to eat from their sacrifice, and you take from their daughters [wives] for your sons, and their daughters whore themselves to other Gods, and your sons whore themselves to other Gods.

"[2] Do not make for yourselves molten¹¹ gods.

"[3] Keep the Feast of the Matsoh, seven days of eating matsoh, whose season, as I commanded to you, is the month 'Abib¹², for in the month 'Abib you went forth from Mitsrayim¹³.

"[4] The firstlings of all wombs are for me: all your firstling male livestock, herdling¹⁴ and flockling¹⁵. But you are to redeem firstling donkeys with flocklings, and whenever you cannot redeem [one], break its neck. Redeem all your firstborn sons and do not face me emptyhanded.

"[5] You are to work for six days, and rest on the seventh day. You must rest [even] in plowing season and in harvest.

"[6] And make for yourselves the Feast of Sevens¹⁶ [with] the first crops of the harvested wheat, and the Feast of the Harvest Gathering at the turnings of the year.

"[7] Three times in a year all your males are to appear before the Lord Yahweh, God of Yishra’el¹⁷. For I will dispossess Goyim in front of you, and I will extend your boundaries, and no man will desire your land when you rise to appear before Yahweh your God three times in a year.

"[8] Do not slaughter to me with yeast [in the] blood of my sacrifice, and do not lodge a sacrifice from the Feast of the Passover through to morning.

"[9] [The] foremost first crops of your ground are to enter into [the] house of Yahweh your God.
[10] You are not to cook a kid¹⁸ in its mother’s milk."

And Yahweh said to Mosheh¹⁹, "Write for yourself these Statements²⁰, for in accord with these Statements I cut a deal with you and Yishra’el." And he was there with Yahweh forty²¹ days and forty nights, not eating food nor drinking water, and he wrote upon the slabs²² the Statements of the Deal²³: The Ten Statements.

—We'eleh Shemoth²⁴ 34:10–28

Footnotes:

1. sometimes translated as "nations"

2. sometimes translated as "LORD", but this is a different word ('adon) whose vowel markings were used over the four letters of YHWH to signify that the name of the god of Israel should not be spoken

3. or "Amorite"—literally, "Speaker"

4. or "Canaanite" or "Phoenician"—literally, "Lowlander"; Canaanites were great sailors and inventors of the alphabet, formulating the script that the scripts for Hebrew, Greek, Latin, etc. derived from.

5. or 'Hittite"—literally, "Son of Heth", "Heth" meaning "Terror"

6. or "Perizzite"—literally, "Rural Villager"

7. or "Hivite"—literally, "Villager"

8. or "Jebusite"—literally, "Son of Yebus", "Yebus" meaning "Trampler"; Jebusites were the founders of Jerusalem

9. Sometimes translated as "groves", but 'Asherah is a goddess, known as 'Astarte in Babylon. Her name is related to the word "straight", hence the meaning here of "'Asherah poles". Although known as the consort of 'El, archaeological evidence suggests she was worshiped by Judahites as the consort of Yahweh.

10. I have render "'el" as "god" and "'elohah" as "God".

11. literally "poured"

12. the first month of Spring, roughly March and/or April

13. Egypt; this is a dual word, possibly reflecting the Upper and Lower Kingdoms

14. e.g., ox

15. e.g., goat or sheep

16. or "Weeks"

17. Israel

18. i.e., a young male goat

19. Moses

20. or, more popularly, "Commandments"

21. literally "fours"

22. or, more popularly, "tablets"

23. or, more popularly, "covenant"

24. "And These Are The Names...", also known as "Exodus"

Inglish av dha Fyuwchrr

Whan that Aprille with his shoures soote
The droghte of Marche hath perced to the roote,
And bathed every veyne in swich licour,
Of which vertu engendred is the flour

—Geoffrey Chaucer

English has changed a lot in the past 600-odd years. None of us will (probably) know how much it will change in the next 600. But I think it's fun to make guesses.

I had an idea once for a way to get an idea of how the sounds of English might change if current trends continue. It was based on the observation that spoken language changes much faster than written language (which is one reason why English is spelled so horribly—the phonology has changed a lot, but we still spell things as Shakespeare might have pronounced them). The basic concept would be to do something like this:

1. Record native speakers, Group A, reading a list of words and phrases out loud. Some of the words should be fictitious, but plausible according to the rules of English phonology and spelling (such as they are).
2. Use a phonetic or phonemic system to write down how Group A pronounced the list.
3. Have another group of native speakers, Group B, read the lists based on Group A's pronunciation. (Note: people in this group must be unfamiliar with the phonetic or phonemic system, and preferably unfamiliar with the study of phonology in general.)
   
4. Extrapolate patterns from the differences in the two groups' pronunciations.

Basically, Group B would be doubling the current disparity between the written language and the spoken language. As an example, the list might provide the word "pight", which someone in Group A might pronounce as /p^haIt/. Someone in Group B, seeing that transcription, might pronounce it as /feIt/ (i.e., "fate"). Then we could extrapolate a p → f trend (which, indeed, already happened in English's cousin, German) and a movement of front diphthongs upward (continuing the work of the Great Vowel Shift). Not a terribly streenge frediction.

Of course, it'd be silly to think that this would be an accurate way of divining the future. Even if it did reflect past trends continuing, that's not always how language evolution works. But it might be a fun exercise to try, nonetheless. We already have reconstructed languages; why not preconstructed?