Wednesday, August 30, 2006

Numerology of Specified Complexity?

Stephen Pinker, Words and Rules, pp. 8-9

"Billions of years ago life on Earth settled on a code in which a string of three bases in a DNA molecule became the instruction for selecting one amino acid when assembling a protein. There are four kinds of bases, so a three-string base allows for 4 x 4 x 4 = 64 possibilites. That is enough to give each of the amino acids [20 of them] its own string, with plenty left over to start and stop instructions that begin and end the protein. two bases would have been too few (4 x 4 = 160, and four more than needed (4 x 4 x 4 x 4 = 256)."

Thursday, August 24, 2006

More on sponges

from NOBEL INTENT
http://arstechnica.com/journals/science.ars/2006/8/18/5040

Our cousin, the sponge. Elaborate multicellular organisms such as us humans require a careful choreography of signaling to generate all the specialized cell types that make up our various organs, and adhesion molecules to hold them together once they're generated. But multicellularity exists across a bit of a spectrum. There are organisms that form aggregates of identical cells, others that can exist both as free living cells or collections of cells that can specialize, and organisms such as sponges, which have specialized cells that are not organized into distinct tissues. Is there any clear dividing line on the evolutionary path that led to us bilateral animals?
A paper in PNAS argues that the answer is yes, and it suggests that we and the sponges fall on the same side of that line. The researchers used a series of completed animal genome sequences to look for cell signaling and adhesion genes, and found that most were distributed throughout all animals. They also looked in yeast, which are unicellular, and slime molds, which can exist as amoebas or in a group with specialized cells. They had almost none of these genes. They then searched a sponge genome, and found that they clearly grouped with the rest of the multicellular animals: in case after case, they had the genes that help us organize our multicellular existence. This also indicates that the genetic raw material for organizing diverse body forms goes back to well before the Cambrian.

phylogentic terms

1.paraphyletic -- Term applied to a group of organisms which includes the most recent common ancestor of all of its members, but not all of the descendants of that most recent common ancestor

-Paraphyletic taxon : A group composed of a collection of organisms, including the most recent common ancestor of all those organisms. Unlike a monophyletic group, a paraphyletic taxon does not include all the descendants of the most recent common ancestor.
Examples : Traditionally defined Dinosauria, fish, gymnosperms, invertebrates, protists, etc.


2.polyphyletic -- Term applied to a group of organisms which does not include the most recent common ancestor of those organisms; the ancestor does not possess the character shared by members of the group. More?

-Polyphyletic taxon : A group composed of a collection of organisms in which the most recent common ancestor of all the included organisms is not included, usually because the common ancestor lacks the characteristics of the group.
Polyphyletic taxa are considered "unnatural", and usually are reclassified once they are discovered to be polyphyletic.
Examples : marine mammals, bipedal mammals, flying vertebrates, trees, algae, etc.



3.monophyletic -- Term applied to a group of organisms which includes the most recent common ancestor of all of its members and all of the descendants of that most recent common ancestor. A monophyletic group is called a clade

-Monophyletic taxon : A group composed of a collection of organisms, including the most recent common ancestor of all those organisms and all the descendants of that most recent common ancestor. A monophyletic taxon is also called a clade.
Examples : Mammalia, Aves (birds), angiosperms, insects, etc.

Wednesday, August 23, 2006

Hips

UCMP website

The saurischian, or "lizard-hipped" dinosaurs, like all other tetrapods, had pelves (hips) composed of three elements: the ilium, ischium, and pubis. What distinguishes saurischians (among other major characteristics; including a grasping hand, asymmetrical fingers, and a long, mobile neck) is the pubis that points downward and forward at an angle to the ischium.

What makes an ornithischian dinosaur? All terrestrial animals and even marine animals derived from terrestrial stocks have hip girdles, or pelvises, and all hip girdles are composed of three bones: the ilium, ischium, and pubis. All ornithischians are united by a pubis pointing backward, running parallel with the ischium. The name "Ornithischia" means "bird-hipped," and birds also have pelvises in which the pubis points backwards. However, birds are more closely related to the Saurischia, or "lizard-hipped" dinosaurs, than to the ornithischian dinosaurs...

[bold added]

Tuesday, August 22, 2006

Geologic Timescale

Holocene
Pleistocene
Pliocene
Miocene
Oligocene
Eocene
Paleocene

Cretaceous
Jurassic
Triassic
Permian
Carboniferous
Devonian
Silurian
Ordovician
Cambrian
Precambrian

Monday, August 21, 2006

Chordates from Columbia

From Bartleby.com (Columbia encyclopedia)

[Chordata]phylum of animals having a notochord, or dorsal stiffening rod, as the chief internal skeletal support at some stage of their development. Most chordates are vertebrates (animals with backbones), but the phylum also includes some small marine invertebrate animals. The three features unique to chordates and found in all of them at least during early development are: the notochord, composed of gelatinous tissue and bound by a tough membrane; a tubular nerve cord (or spinal cord), located above the notochord; and gill slits leading into the pharynx, or anterior part of the digestive tract (the throat, in higher vertebrates). In addition, all have blood contained in vessels, and the tunicates and vertebrates have a ventrally located heart. All have a postanal tail, that is, an extension beyond the anus of the notochord or backbone and of the body-wall musculature, containing no internal organs.

[Verbrates] can be traced back to the Silurian period. In the adults of nearly all forms the backbone consists of a series of vertebrae. All vertebrates belong to the subphylum Vertebrata of the phylum Chordata. There are five classes of vertebrates: fish, amphibians, reptiles, birds, and mammals.
There are eight vertebrate classes. Four are aquatic, and may be grouped together as the superclass Pisces, or fish; four are terrestrial or (in the case of amphibians) semiterrestrial, and may be grouped as the superclass Tetrapoda, or four-footed animals.
There are two invertebrate subphyla: the Urochordata, or tunicates, and the Cephalochordata, or lancelets. A third invertebrate group, comprising the acorn worms and their relatives, shows affinities with chordates and has sometimes been considered a chordate subphylum, but is now often classified in a phylum of its own, the Hemichordata.
[Invertebrates] any animal lacking a backbone. The invertebrates include the tunicates and lancelets of phylum Chordata, as well as all animal phyla other than Chordata. The major invertebrate phyla include: the sponges (Porifera), coelenterates (Cnidaria), echinoderms (Echinodermata), flatworms (Platyhelminthes), roundworms (Nematoda), segmented worms (Annelida), mollusks (Mollusca), and arthropods (Arthropoda). Invertebrates are tremendously diverse, ranging from microscopic wormlike mezozoans (see Mezozoa) to very large animals such as the giant squid. Approximately 95% of all the earth’s animal species are invertebrates; of these the vast majority are insects and other arthropods. Invertebrates are important as parasites and are essential elements of all ecological communities.

Wednesday, August 16, 2006

Chordates

from UCMP website

Bilateria-Deuterostomia-chordates, echinoderms

All chordates have the following features at some point in their life (in the case of humans and many other vertebrates, these features may only be present in the embryo):


pharyngeal slits - a series of openings that connect the inside of the throat to the outside of the "neck". These are often, but not always, used as gills.

dorsal nerve cord - a bundle of nerve fibers which runs down the "back". It connects the brain with the lateral muscles and other organs.

notochord - cartilaginous rod running underneath, and supporting, the nerve cord.

post-anal tail - an extension of the body past the anal opening.

"In bilateral invertebrates the nerve cord is ventral to the alimentary canal or gut... [vertebrates, in which the spinal cord is dorsal, the gut lying ventral to it]" [my brackets]

O'Shea, The Brain p.47

Porifera

PORIFERA
from UCMP website

"An early branching event in the history of animals separated the sponges from other metazoans. As one would expect based on their phylogenetic position, fossil sponges are among the oldest known animal fossils, dating from the Late Precambrian.
Poriferans don't have mouths; instead, they have tiny pores in their outer walls through which water is drawn. Cells in the sponge walls filter goodies from the water as the water is pumped through the body and out other larger openings. The flow of water through the sponge is unidirectional, driven by the beating of flagella which line the surface of chambers connected by a series of canals"

Fossils: "the first probable sponge, Paleophragmodictya, from the Ediacara of Australia"

Sponges reproduce by both asexual and sexual means. Most poriferans that reproduce by sexual means are hermaphroditic and produce eggs and sperm at different times.

"Sponges have a cellular grade of organization. They do not possess any structures that can be considered organs. For instance, sponges do not have stomachs or kidneys. Instead, sponge cells of various types are responsible for bodily functions, the day-to-day activities that sustain life. Many of the most common types of cells are illustrated below in a cartoon view of the wall of a poriferan. "

http://www.ucmp.berkeley.edu/porifera/pororg.html here

Choanocytes (one of the 7 types of cells found in sponges)
"These distinctive cells line the interior body walls of sponges. These cells have a central flagellum that is surrounded by a collar of microvilli. It is their striking resemblance to the single-celled protists called choanoflagellates that make many scientists believe that choanoflagellates are the sister group to the animals. Choanocytes are versatile cells. Their flagella beat to create the active pumping of water through the sponge, while the collars of the choanocytes are the primary areas that nutrients are absorbed into the sponge. Furthermore, in some sponges the choanoflagellates develop into gametes. "


sponges: no nervous system; cells not organized into tissues; toti-potent cells, any cell can grow a new sponge. no distinction between germ & soma, as in eumetazoa [the rest of the metazoa].

sponge & placyzoa most primitive living group of multi-cellular animals; sometimes classed as parazoa for this reason
Dawkins, AT, p.497-501

porifera (fm choanomonads),ancestor to coelenterates, Mayr, WEI, p52-3

Tuesday, August 15, 2006

Ring Species

RING SPECIES
Salamanders Ensatina eschscholtzii, Ensatina klauberi (Central Valley, California)Diagram Mayr, WEI, p.184

herring gull, lesser black-backed gull Larus argentatus, Larus fuscus
Dawkins, AT, p.311


POLYTYPIC SPECIES
Kangaroo rat. Mayr, WEI,p.164, diagram. 35 sub-species Western USA.

Monday, August 14, 2006

Some basic framework

Cambrian explosion: 543mya. Beginning of Phanerozoic EON, Paleozoic ERA, Cambrian PERIOD.

EPOCH: we live in the Holocene Epoch. Epoch is a subdivision of Period.

Phanerozoic EON: Paleozoic, Mesozoic, Cenozoic ERAS.
Permian extinction at end of Paleozoic, mass extinction at end of Cretaceous period (65mya), Mesozoic era.

LINNAEAN HIERARCHY
Domain, Kingdom, Phylum, Class, Cohort, Order, Family, Subfamily, Tribe, Genus, Species, Subspecies. (Mayr, WEI, p.23 (except for Domain [UCMP]).

Georgia Purdom at YEC Conference

Jason Rosenhouse in Skeptic magazine, Vol.12, #2, pg.15, discussing a talk by Georgia Purdom at a Young Earth Creationist Conference:

"Purdom began by arguing that ID poses grave problems for Christians by taking no stand on the nature and specific actions of the designer. She discussed the natural theology of the 18th and 19th centuries, presenting it as an argument that we could have knowledge of God apart from the Bible."

"Purdom then argued that natural theology backfired because it led to deism."

"She argued that another problem with ID is that it provides no account of poor design. She pointed to pathogenic microbes, carnivorous animals, and viruses. She said that ID makes God Himself the author of such natural evil, instead of original sin being the culprit."

Of course these quotes are from Rosenhouse, not Purdom herself.

Sunday, August 13, 2006

blastopore

Some definitions from Bartleby.com reference dictionary

BLASTULA
NOUN: Inflected forms: pl. blas·tu·las or blas·tu·lae (-l)
An early embryonic form produced by cleavage of a fertilized ovum and consisting of a spherical layer of cells surrounding a fluid-filled cavity. Also called blastosphere.
ETYMOLOGY: New Latin : from Greek blastos, bud + Latin -ula, feminine diminutive suffix

It is a hollow ball of cells, one cell thick. (Dawkins, below)

BLASTOPORE
NOUN: Embryology The opening of the archenteron.

GASTRULA
NOUN: Inflected forms: pl. gas·tru·las or gas·tru·lae (-l)
An embryo at the stage following the blastula, consisting of a hollow, two-layered sac of ectoderm and endoderm surrounding an archenteron that communicates with the exterior through the blastopore.
ETYMOLOGY: New Latin : Greek gastr, gastr-, belly + Latin -ula, feminine diminutive suff

GASTRULATION
NOUN: The process of forming a gastrula.

ARCHENTERON
NOUN: The central cavity of the gastrula, which ultimately becomes the intestinal or digestive cavity.

In protostomes (mouth first) the blastopore becomes the mouth (or both mouth and anus. In deuterostomes (mouth second) the blastopore becomes the anus.

590mya?

See Dawkins, AT, pp.387-89

Saturday, August 12, 2006

Placyzoa

Trichoplax adhaerans has 1 Hox Gene, 4 different types of cells.

Dawkins, AT, p.494

Thursday, August 10, 2006

Fossil Fungi

"Fossil fungi older than the Devonian are rare; the fungi may have undergone an evolutionary radiation at about the same time that the land plants began to radiate."
UCMP fungi

Wednesday, August 09, 2006

Protozoan

Protozoan, single-celled animal, an obsolete term for a sub-kingdom.
Cyanobacteria: green bacteria, blue-green bacteria.