28 February 2013

Another "All Your Yesterdays" entry: Denisovan, or "Polar Neandertal"

They've extended the deadline for the All Your Yesterdays contest, so I've decided to do a couple more entries. I started this one years ago as a Neandertal restoration. Since that time, new genomic discoveries showed that the speculative pigmentation was incorrect. But, other discoveries identified a new candidate for the subject matter!

Known from a few scrappy pieces, the Siberian Denisovans (Homo sp. or Homo sapiens ssp., depending on how large you like your species) are a true challenge to reconstruct. We have their entire genome, but know almost nothing about their anatomy. The few fossil elements we have are not morphologically distinct from Neandertals (Homo neanderthalensis or Homo sapiens neanderthalensis) or humans (Homo sapiens sapiens).
But the genomic facts are highly intriguing:
  1. Some Oceanian humans have inherited up to 6% of their nuclear DNA from Denisovans (with the highest ratios in Meganesia [Australia and New Guinea]). 
  2. The nuclear DNA indicates a common ancestor with Neandertals, shortly after the split from proto-humans.
  3. But the mitochondrial DNA indicates a motherline that branched off much earlier. (Possibly Homo erectus?)
  4. Genes for pigments are consistent with dark skin.
Here I've imagined a Siberian Denisovan as a sort of "polar Neandertal". As with polar bears, his skin is dark, trapping heat, but his pelage is light, allowing for camouflage against the taiga and tundra. He is the last of his kind — his southern kin mixed with the strange, baby-faced people who keep invading from the west. But he does not welcome them. He will fight to his death.

27 February 2013

"Texan Mama", my "All Your Yesterdays" contest entry

I would have worked on this a bit longer, but the "All Your Yesterdays" contest deadline is tomorrow.
Texan Mama
Dimetrodon and its kin have often been described as "mammal-like reptiles", but in fact they they are just as closely related to modern reptiles as we are (in terms of shared descent). Creatures like Dimetrodon, Moschops, Lystrosaurus, Cynognathus, Morganucodon, etc. are more properly termed "stem-mammals", meaning that they are not mammals, but are more closely related to mammals than to any other living organisms.

We can infer, in the absence of direct evidence, that all stem-mammals probably possessed any characteristics shared by us mammals and our closest living non-mammalian relatives, the sauropsids: turtles, tuataras, lizards (including snakes), crocodylians, and birds. But mammalian characteristics not shared by sauropsids are trickier. When did hair evolve? When did lactation evolve? We have a few clues but no definite answers.

In this piece, I have pushed fur back to an extremely early time — Dimetrodon is one of the furthest stem-mammals from Mammalia proper. While we know that a later stem-mammal, Estemmenosuchus, had glandular skin without any sign of fur, it is possible that fur evolved earlier and was simply lost or reduced in some lineages, as it has been in many lineages of placental mammal.

I have also posited parental feeding, but not, strictly speaking, lactation. Other lineages of tetrapod, including caecilians and pigeons, have evolved ways of feeding the young from foodstuffs produced by the mother. The mother Dimetrodon's sides are swollen with nutritious substances which seep out as her pups gobble it up. Is it milk? Sort of and sort of not.

Finally, I have scrupulously avoided any suggestion that these are in any way reptilian. They do retain some plesiomorphies evidenced in some reptiles, amphibians, and lungfishes, such as a sprawling gait, belly scales, and acute color vision, but they lack the dry skin and derived scales of true reptiles. Not a single sauropsid texture was used in the photocollage; instead they have the textures of Hippopotamus, Phacochoerus, Procyon, Homo, Zaglossus, Caecilia, Litoria, and even Neoceratodus. These Dimetrodon are moist, glandular creatures — not reptiles at all.
If you're wondering, here's a quick breakdown of the textures used:
Hippopotamus amphibius (hippo)
general, especially mother's head and torso
Phacochoerus (warthog)
general, especially mother's tail and torso
Procyon (raccoon)
Homo sapiens (human)
general, especially mother's sail
Zaglossus (long-beaked echidna)
juveniles' faces
Caecilia (caecilian)
mother's sides and underside
Litoria caerulea (Australian green tree frog)
general, especially mother's limbs
Neoceratodus forsteri (Queensland lungfish)
juveniles' underbelly
I've also submitted a variant, done in a Pop Art style inspired by Roy Lichtenstein's work, to the related Love in the Time of Chasmosaurs: All Yesterdays contest:

Note: Yes, I do descend from a long line of Texan mothers.

15 February 2013

JSEN: JavaScript Expression Notation

That idea I was talking about yesterday? Storing mathematical expressions as JSON? I went ahead and made it as a TypeScript project and released it on GitHub:

JavaScript Expression Notation (JSEN)

Still need to complete the unit test coverage and add a couple more features. I made a change from my original post to the syntax for namespace references. (The reason? I realized I needed to be able to use "*" as a local identifier for multiplication.) They work within Namespace declaration blocks, but I need to make them work at the higher level of Namespaces declaration blocks as well. (Done.) I also want to allow functions to be used as namespaces. (Done.)

This is possible right now:

jsen.decl('my-fake-namespace', {
   'js': 'http://ecma-international.org/ecma-262/5.1',

   'x': 10,
   'y': ['js:Array', 1, 2, 3],
   'z': ['js:[]', 'y', 1]

jsen.eval('my-fake-namespace', 'x'); // 10
jsen.eval('my-fake-namespace', 'y'); // [1, 2, 3]
jsen.eval('my-fake-namespace', 'z'); // 2

jsen.expr('my-fake-namespace', 'x'); // 10 // Deprecated
jsen.expr('my-fake-namespace', 'y'); // Deprecated
    // ["http://ecma-international.org/ecma-262/5.1:Array", 1, 2, 3]
jsen.expr('my-fake-namespace', 'z'); // Deprecated
    // ["http://ecma-international.org/ecma-262/5.1:[]", "y", 1]

Eventually something like this will be possible as well:

14 February 2013

Mathematical expressions as JSON (and phyloreferencing)

For Names on Nodes I did a lot of work with MathML (specifically MathML-Content), an application of XML for representing mathematical concepts. But now, as XML wanes and JSON waxes, I've started to look at ideas for porting Names on Nodes concepts over to JSON.

I've been drawing up a very basic and extensible way to interpret JSON mathematically. Each of the core JSON values translates like so:
  • Null, Boolean, and Number values are interpreted as themselves.
  • Strings are interpreted as qualified identifiers (if they include ":") or local identifiers (otherwise).
  • Arrays are interpreted as the application of an operation, where the first element is a string identifying the operation and the remaining elements are arguments.
  • Objects are interpreted either as:
    • a set of declarations, where each key is a [local] identifier and each value is an evaluable JSON expression (see above), or
    • a namespace, where each key is a URI and each value is a series of declarations (see previous).


Here's a simple object declaring some mathematical constants (approximately):

    "e": 2.718281828459045,
    "pi": 3.141592653589793

Supposing we had declared some operations (only possible in JavaScript, since JSON doesn't have functions) equivalent to those of MathML (whose namespace URI is "http://www.w3.org/1998/Math/MathML"), we could do this:


Once evaluated, x would be 3 and y would be 1 (or close to it, given that this is floating-point math).

Now for the interesting stuff. Suppose we had declared Names on Nodes operations and some taxa using LSIDs:

    "Homo sapiens": "urn:lsid:ubio.org:namebank:109086",
    "Ornithorhynchus anatinus": "urn:lsid:ubio.org:namebank:7094675",
                "Homo sapiens",
                "Ornithorhynchus anatinus"

Voilá, a phylogenetic definition of Mammalia in JSON!

I think this could be pretty useful. My one issue is the repetition of  long URIs. It would be nice to have a mechanism to import them using shorter handles. Maybe something like this?

    "mathml":   "http://www.w3.org/1998/Math/MathML:*",
    "namebank": "urn:lsid:ubio.org:namebank:*",
    "NoN":      "http://namesonnodes.org/ns/math/2013:*",


Something to ponder. Another thing to ponder: what should I call this? MathON? MaSON?