Prepared July, 2010


       

In Celebration of Psalm Nineteen:
God's handiwork in Creation

Chapter 11

CREATION OF THE ANIMAL PHYLA

AND DEVELOPMENT GENE PACKAGES

IN THE CAMBRIAN EXPLOSION

"The Magnates Walk First" -- Hugh Miller


"We must suppose that when the Author of Nature creates an animal or plant, all the possible circumstances in which its descendants are destined to live are foreseen, and that an organization is conferred upon it which will enable the species to perpetuate itself and survive under all the varying circumstances to which it must be inevitably exposed."
Lyell, Principles of Geology (1850)
Ch. 35: Transmutation of Species, p. 560

"Why should the enlightened Christian, who has a correct idea of the firm foundation on which the Bible rests, fear that any disclosures of the arcana of nature should shake its authority or weaken its influence? Is not the God of revelation the God of nature also?"
Edward Hitchcock Religion of Geology (1851), p. 38



UNDER CONSTRUCTION

NOTE:  Chapters 9-11 will be reorganized in the final version.




first trilobites

What is the distinction between a multi-cellular colony and a multi-cellular species???  Cell to cell signalling? What does it?
cyanobacteria

Timeline of plant evolution







In this chapter we will first discuss the



CHECK:
"alternation of generations"
haploid/diploid - Tudge p. 24. diploid = ? double chromosomes?
haploid/diploid  stages of life. In sexual animals: diploid is normal. egg and sperm are haploid, and join at fertilization to form a diploid.

mosses: normally haploid. Then two separate cells "mate" and form temporary diploid which forms next generation *& again haploid (???)
most other plants: diploid is normal stage just as most animals.




haploid = only half there.




With the creation of the eukaryotic cell, multi-cellular plants and animals can be made.

\



fractal

http://en.wikipedia.org/wiki/Geologic_timescale


fractal
MOVE UP


In Celebration of Psalm Nineteen:
God's handiwork in Creation

CREATION OF MARINE ANIMALS

UNDER CONSTRUCTION

ANIMALS:
• Hox expression
etc.



-- In the Interim

Throughout the time between the first life and the appearance of visible, multicellular life, all living species had the task of filling the globe with organic nutrients. The more complex the life form, the less it could afford to take the time or energy to create its own food. Thus there had to be readily available food -- fixed nitrogen, amino acids, nucleotides, sugars, etc. -- so that the complex species could concentrate their energies on more advanced tasks. This filling of the earth took a long time, and this is the primary reason why the first appearance of visible animals in the Cambrian explosion around 550 Ma took place  over three billion years after the first living cell appeared on earth.

-- Multi-Cellular Life -- the Cambrian Explosion36.

There is fossil evidence of multi-celled species forming much earlier than the Cambrian era (around 550 Ma). The use of differently specialized cells goes back to the very earliest life (for nitrogen fixing and other specialized tasks). The signature thing that distinguishes multicellular species is the use of many copies of a specialized cell type, and the development of inter-cellular signaling mechanisms so that the many cells can act in coordination.

Since all living species start out as a single cell, this implies that the dna for the species must include genes for all of the specialized cell types, and must have a expression genes that program the cell specialization as the embryo develops. 

Animals differ from plants in that they have a much more elaborate body plan that is built into the embryonic development. This plan is incorporated into the homeobox or "hox" genes and expression or development genes. The various animal phyla differ in the organization of these genes, and the resulting complexity of the species. These are responsible for the left-right symmetry that higher animals often possess, and for the differentiation of the cells into the various organisms of the body. 

[Topology in development of body plans]

The irony, from the perspective of natural evolution, is that all of the basic animal body plans appear almost simultaneously within about a 10 My span of time about 550 Ma.  Recent work on development genes indicates that at this time, a number of basic gene packages appear which were used over and over in many combinations during the subsequent development of animal life.  For example, there are development gene packages to control the development of appendages, of eyes, of the nervous system. These same packages are used repeatedly in different configurations over the next 500My.


Multi-celled plants arose first in the

IT APPEARS THAT the plant phyla arose over a much longer period of time than did the animal phyla, which appear to have arisen fairly rapidly in the Cambrian Era (nominally 550-500 Ma). In large part this may be due to the fact that most plant phyla arose on dry land, and life on land was difficult if not impossible prior to the build-up of an effective ozone layer around 400 Ma which filtered out most harmful "hard" (ultra-violet and higher energy) cosmic and solar rays.




The Trilobites

Trilobites appear in the early Cambrian era, the oldest stratum of "visible" hard-shelled fossils (the Phanerozoic eon, beginning about 545 Ma). They first appear as complete, fully-developed arthropods. They are unique among the Arthropods in that the body plan consists of 3-lobed segments (hence the name), but otherwise they have features similar to modern Crustaceans.


Perhaps trilobites are the most famous of the early fossils. They first show up as fully formed complex fossils in the early Cambrian Era (521 Ma) and become extinct in the Permian Era (251 Ma) in a clataclysmic extinction that marks the end of the Palaeozoic Age, after about 300 million years. Thus the abundant and very long trilobite fossil record is an opportunity to observe the great range of species changes that can occur over a very long time[FOOTNOTE: For illustration of the changes, see S.M. Gon III, Evolutionary Trends in Trilobites].

trilobite Early Cambrian
Figure ??
Early Cambrian Trilobite

Evidence for Evolutionary Development. If one assumes that the observable changes in trilobite species over the 300 My of the fossil record amount to an extended example of Evo-Devo[FOOTNOTE: Evo-Devo attributes evolutionary change to changes in gene expression of a limited number of highly conserved genes. The gene expression is controlled by homeobox (hox) genes (also conserved, although not so highly as the gene packages) combined with development parameters that are recorded in the portions of DNA that do not code for genes]  (which I do), then this long record gives a good opportunity to examine the implications of such potential for change, and is a good example of how the Silent Speech of Psalm 19 is woven into the natural world. Of course it is not possible to study this development at the genetic level on trilibotes themselves, but it should still be possible to reduce the observed changes into plausible hypotheses that can be tested in the laboratory using living species.

Recent work in Evo-Devo implies that most animal species -- extending back to the first appearance in the Cambrian era -- use a small packages of genes in the development of eyes and appendages (and, I suspect, many other major systems). These gene packages are virtually identical across a broad swath of species within and across many radically different body plans (phyla). The differing end results are the result of homeobox (hox) gene expression, which follow instructions contained in portions of the DNA that do not code for genes. Apparently, the instructions are subject to some natural variation, and the variations can be passed to future generations. The beneficial (or neutral) variations tend over time to survive and the unbeneficial variations tend to die out. These give rise over time to different families, genera and species[FOOTNOTE: The use of DNA profiling to identify individuals is based on variations between individuals in non-coding portions (so-called "junk" dna)].

A surprising conclusion of Evo-Devo work is that many animal features that appear to be quite different, in fact are at root different expressions of the same underlying gene packages: such as, for example, compound eyes and simple eyes, and even focusing and non-focusing eyes. The trilobites display a broad variety of eyes over their long history, and these appear (I assume) to be the accumulation of small variations in gene expression of the basic (and largely unchanging) gene package for eye development.
For example, at another place I argue that computer simulation might be able to investigate testable hypotheses that emulate the evolution of the trilobite eye from a conical shape (the holochroal eye) to the bi-layered elliptical or spherical shape (the schizochroal eye) -- a case, I believe, of paedomorphosis.

Life Cycle. Most trilobite fossils are trilobite molts. Trilobites molt repeatedly nearly from the time they hatch, which shows how they grow and mature. Thus the fossil record provides abundant documentation of the growth and molting process.

Soft-body parts. Normally, details of soft-body parts are not preserved in fossils. Discovery of pyritized trilobites provides another example of the Silent Speech. By a miraculous preservation, some trilobites discovered near Rome, New York (and a few other places globally) have had the hard and soft-body parts replaced by finely crystaline pyrite (FeS2) (commonly known as fool’s gold because of its golden color). They display finely detailed external appendages and gills. X-rays reveal details of soft tissue -- muscular, digestive, nervous and circulatory systems. As a result of this providential gift, much is known about trilobite anatomy despite the fact that they have been extinct for 250 million years (Figure ??)
[FOOTNOTE: Rolf Ludvigsen, Fossils of Ontario Part 1: the Trilobites, Royal Ontario Museum, 1979, pg. 22. Also see various internet discussions of pyritized trilobites.].

trilobite anatomy
Figure ??
Trilobite Anatomy





Silent voice
anticipatory gene packages (these, molluscs, insects), hox gene scheme

appendage package: antennae, jointed legs, gills, senses (touch, ???)
eye package


flexible dev't -- not yet specialized (cf remarks by ??? about pattern of specialization in fossil record).

[cf rmk by Gon] Begin general, develop to special. GET WUOTE






changes over the 200 My of existence: number, location (some on stalks) & type of compound eyes.

Systems:
appendages - jointed legs, claws, antennae (appear to be genetically controlled by similar gene package)
respiration - gills
vision - compound eyes (change over the existence)
senses: vision, smell, touch, hearing?,
muscular -
nervous - ganglia, primitive brain?
circulatory -
primitive digestive system - lack chewing parts, proper stomach, etc.



I believe the Creator left this fossil record so that we could learn how much variation natural processes generate. As time passes, I believe that many details will be filled into the narrative. Already scientists are discovering something about the range of possibilities in the formation, location and type of eyes and the various appendages (antennae, legs).

It is useful to keep in mind that the distance between species may not be so close to appearance as might be thought. The maturation of a species is a complicated function of the gene pool and the gene expression (gene regulation). Laboratory experiments demonstrate that very small changes can result in radically different expression. For example, two trilobite species with radically different numbers of compound eyes (say, 500 or 5000) may not in fact be very far apart genetically: it boils down not to radically different genetic code, but to a difference in when the genetic expression was "turned off." An analogy would be in the difference between a faucet producing a cup of water and a bucket of water: we are not talking about radically different faucets, but just when the faucet was turned off. On the other hand, the difference between a cup of water and an ocean of water is probably a radical difference.



PRE:CAMBRIAN FOSSILS IN THE Chengjiang (Cambrian) & Dengying (Ediacarian) Formation of southern Chins.

NOTE THAT THE PHYLA DESIGNATIONS ARE NAMED IN APPROXIMATE ORDER OF COMPLEXITY, BUT THAT THIS IS NOT THE ORDER OF OCCURRENCE IN THE FOSSIL RECORD.




Common Animal Phyla Originating in the Cambrian Explosion (~542-530 Ma)
The Phyla designations listed here are in approximate order of complexity.*


Buckland on Fossils and the Cambrian Explosion
Beginning with the animal kingdom, we find the four great existing divisions of Vertebrata, Mollusca, Articulata, and Radiata, to have been coeval with the commencement of organic life upon our globe.…all of the four existing great Classes of the grand Division of Articulated animals, viz. Annelidans, Crustaceans, Arachnidans, and Insects, and many of their Orders, had entered on their respective functions in the natural world, at the early Epoch of the Transition Formations.” [p.413]

“It has not been found necessary, in discussing the history of fossil plants and animals, to constitute a single new class; they all fall naturally into the same great sections as the existing forms.” [p. 61 quoting phillip's Guide to Geology, pp. 61-63]
William Buckland, Geology and Mineralogy Considered with Reference to Natural Theology (1835)
Bridgewater Treatise, Vol. VI













designation*   
Name, Meaning*   
Features
 Examples Fossils
Innovations prior to the appearance of multi-celled plants/animals in the Ediacarian era (630-542 Ma):  photosynthesis -- ATP, sucrose, proton pump; nitrogenase, akinetes (spores), heterocysts; asexual cell division. These arose in bacteria as early as 3,500 Ma.  Cytoskeletons arose with single-celled eukaryotes around 1,500 Ma.  Sexual reproduction  may also have arisen  as early as ????.  Meiosis/mitosis? req's cytoskeleton?

All animal phyla are multi-cellular, oxygen-breathing (aerobic) eukaryotes. All develop from a blastula.

Single-celled eukaryotes are classified as Protoctista, with an uncertain date of origin, probably beginning around 1,750 Ma. No eukaryotes are able to fix nitrogen. [INSERT
Aside on Life cycle of "colonial" amoebas]. All protoctista are aerobic except Pr-1. All are aquatic (requiring at least moisture).
 Pr-1 to Pr-36
Protoctista "first established"

Single-celled Eukaryotes Amoebas (Pr-2, Rhizopods),
Foraminifera (Pr-3)
Paramecia (Pr-6)
Slime molds (Pr-23)
Brown Algae, Kelps (Pr-17)
Green Algae (Pr-28)
Red Algae (Pr-33)
Ediacara,
Cambrian,
Carboniferous
Subkingdom Parazoa (A-1 to A-3) lack organs and are generally of indeterminate form.
A-1
Placozoa "flat animal"
barely visible; no organs, no form


A-2
Myxozoa
microscopic; form spores


A-3
Porifera "porous"
cells not organized into tissues;
no digestive gut; current flow
through pores draws food
Sponges
Cambrian
Origin: Precambrian. Many varieties in Cambrian.
Features: Cells are not organized into tissues.
Innovation: Spongin, a protein made of modified collagen. Sexual  and asexual cell division.
Aside on Cell Division.
A-4
Colenterata "hollow intestine"
Cnidaria "stingers"
stingers (nematocysts), differentiated tissues,
 nerves;  sexual, asexual "budding"
corals, hydras, medusas
jellyfish
Cambrian
Origin: Precambrian or Cambrian. Many varieties in the Cambrian.
Features: Stingers (nematocysts are a defining feature); blind body cavity for digesting food; radial symmetry; Colony of specialized species: gastrozooids which process food and trozooids which are mouthless and pass food to the gastrozooids; reproductive zooids (ampullae).
Innovation: Simple body plan (radial symmetry); true tissues - central digestive cavity (hydras); simple nerve network; senses - feeling, taste; stingers (nematocysts); non-muscular contraction;  pseudopods. Reproduction by asexual budding but also sexual.
Aside on the engineering of stingers.
A-5
Ctenophora "combs"
comb bearing; coiled tentacles
comb jellies

Origin: Precambrian
Features: bilateral symmetry
Innovation: nerve network; smooth muscle
Fossil from Chengjiang formation
A-6
A-7
Gnathostomulida "jaw worms"
Platyhelminthes "flatworms"
mouth with jaws and teeth
genitalia
horsehair worms
fossilize poorly
Origin: fossilize poorly
Features: genitalia; mouth with jaws and teeth; three tissue layers, no anus.
Innovation: genitalia; mouth with jaws and teeth; three tissue layers (epidermis - ecktoderm, mesoderm - muscles, etc., digestive cavity - endoderm)

A-10
A-11
A-12

Nematoda "thread"
Nematomorpha

thread forming
horsehair worms
round worms

Origin: Pr
Features:
Innovation: Full digestive system (mouth, intestines, anus); molting;  sense organs (chemical); separate sexes; internal fertilization
Fossil from Chengjiang formation.
A-14
Rotifera
wheel (beating cilia appear rotating)
“wheel animacules”

Origin: Pr
Features:
Innovation: Eye spot; stomach; glands

A--15 to A-19 are various parasites and small creatures - lots of worms!
Arthropods ("jointed foot") are phyla A-20 and A-21. Phyla A-1 to A-19 all lack proper appendages -- legs and antennae. Most of the phyla beginning with A-20  have these appendages (possibly excluding A-22 to A-25. In some cases, appendages are absent or diminished because they are vestigal -- snake "legs", for example). Legs and antennae have received much study in the recent science of  Evolutionary Development. An astounding result of this early work (and we still are in the early days of that science!) is that appendages develop from a limited package of genes that is nearly identical across all of the animal phyla A-20 and higher. The broad range of expression of this limited package of genes is controlled by how the genes are expressed, and that is a function of another package of regulatory genes found in all higher animals, the homeobox (hox) genes, together with various instructions that are part of the so-called "junk" DNA. The regulatory genes determine when, where and how genes are expressed. Other highly conserved gene packages also are known -- for eye development, for example. Although the science is still in its early days, it appears that these conserved gene packages trace back to the Cambrian Era, and they have been very little changed since that time (although the expression of the genes has changed radically).
A-20
Chelicerata "claws"
class Arachnida
Arachnida = goddess Arachne
scorpions, spiders
horseshoe crabs, trilobites
Early Cambrian
Origin: Pre-cambrian, Cambrian (trilobites)
Features: Trilobites are the first animals to have eyes. They are the only species to have crystaline eyes (calcite). The eyes are compound. The appendage gene package. Repeated segmentation, molting.

Note: Evo-Devo indicates that compound and simple eyes share the same basic gene package. Similarly, jointed appendages and antennas develop from the same gene package. These basic gene packages appear to be virtually unchanged across many phyla and classes.

Innovation: Segmented (repeated) body plan (characteristic of all higher phyla); Jointed legs, antennae; thru-gut; blood circulation with heart; nervous and developed muscular system; molting exoskeleton; gills.

A-20
Mandibulata
chewing jaw termites, insects,daddylonglegs

Origin:
Features:
Most of the basic gene packages for future EvoDevo appear to be present in the trilobites.
Innovation: jointed legs, antennae, eyes, gills, multi-layered exoskeleton consisting of:sensory hairs, waxy outer layer, calcified hard middle layer, flexible chitinous inner layer, skin; molting, bilateral symmetry; musclar, nervous (ganglia), circulatory (heart), digestive systems.

A-21
Crustacea
shelly, crusty insects, barnacles, lobsters, crabs,
scorpions, butterflies

Origin: Pr
Features: Body segmentation into head, thorax and abdomen (+ tail?). mandibles (chewing jaws).
Innovation: Sp

A-22
Annelida
ring (segments)
earthworms

Origin: Cambrian
Features: tough outer layer (cuticle) which fossilizes. Some have hard jaws.
Innovation:  developed muscular & nervous system

A-23 to A-25
Pogonophora (Hyolitha)
beard bearing
tube worms

Origin: Fossil Phylum Hyolitha is placed here by Margullis.
Features:
Innovation: Sp
Fossil from Chengjiang formation37

A-26
Mollusca
soft body
snails, clams, octopus
Knightoconus,class monoplacophora; perhaps the oldest "living fossil."
snail A. attleborensis (class gastropoda)
Origin: Precambrian, but first clear mollusc fossils are early Cambrian.
Features: hard shell, muscular foot, gills, circulatory system with heart, liver.
Innovation: Shells (univalve, bivalve)

A-27
Tardigrada (Lobopodia)
slow step
water bears, fossil Lobopodia

Origin: Fossil Phylum  is placed here by Margullis.
Features:
Innovation: Sp
Fossil from Chengjiang formation37

A-30
Brachiopoda
“arm leg” tentacles
lampshells

Origin: Lingula - early Cambrian. One of longest extant phyla -- 600+ Ma.
Features: Two-part dissimilar shells. mantle-secretes shell; brachia, stalk (pedicule).
Innovation: Armor protection; muscles, blind digestive tract, nerves, ganglia, sometimes heart.

A-34
Echinodermata = hedgehog skin

starfish, crinoids

Origin: Pr
Features: Cel.
Innovation: Sp

A-37
Craniata
(all modern species are vertebrates)
brain
fish, amphibians, reptiles, birds,
mammals

Origin: Pr
Features: Cel.
Innovation: Brain residing in cranium; notocord or spinal column; sexual reproduction;

* Following the nomenclature of Lynn Margulis et al, Kingdoms and Domains, Academic Press, 2009 (4th Edition, previously titled Five Kingdoms). "The animal phyla are described here in approximate order of increasing morphological complexity." [p. 237]

This nomenclature includes all vertebrates as Craniata; some extinct vertebrate species did not have Crania.







Animal Body Systems
1. Regulatory
a. Body topography - orientation, symmetry, segmentation, etc.
b. Body parts -- appendages, defenses (stingers, claws, etc.)
c. Glands (skin) etc.
d. Life cycle
2. Digestion
a. Gastrovascular cavity -- one opening
b. Digestive tract (gut) -- two openings (mouth for food intake, coelom for digestion, anus for elimination)
3. Respiration - intake of oxygen, release of carbon dioxide
a. Diffusion across moist surfaces (earthworm)
b. Gills in aquatic animals
c. Lungs in terrestrial animals
4. Circulation - transport of oxygen and nutrients throughout the body
a. Open circulatory system -- some vessels; body cavity is "washed" with blood and lymph
b. Closed circulatory system -- blood enclosed in vessels, capillaries deliver to organs, recycled to heart.
5. Muscular
6. Nervous system -- coordinate activities of the body
a. Neurons -- nerve cells that send impulses
b. Nerve net -- network of neurons, very little coordination
c. Ganglia -- clusters of neurons (simple brain)
d. Brain -- sensory structures and neutrons located at anterior end, complex coordination and behavior.
7. Sensory systems -- (part of nervous system?)
a. Sight
eyespots
b. Hearing
c. Smell
sensory pits
d. Taste
e. Feel/Touch
8. Support -- maintain body shape and support, aid in locomotion
a. Hydrostatic skeleton -- water pressure (jellyfish, worms)
b. Exoskeleton -- outside skeleton (insects, crabs)
c. Endoskeleton -- internal skeleton (vertebrates)
9. Reproductive (Genital)
a. Asexual -- reproduction of offspring from one parent. Offspring are idenical
(1). Regeneration -- fragmentation and regrowth (sponges)
(2). Budding -- growth and release of a clone (hydras)
(3). Parthenogenesis (rare) -- individual develops from unfertilized egg
b. Sexual -- reproduction by mating egg and sperm. One or two parents.
(1). Hermaphrodite -- single parent produces both egg and sperm (earthworm)
(2). External fertilization -- sperm and egg released into water.
(3). Internal fertilization -- sperm and egg mate within the female body.
10. Gestation
a. External (eggs, etc.)
b. Internal

Phyla
as
Fossils
as









fractal

NOTES
http://en.wikipedia.org/wiki/Timeline_of_plant_evolution

the role of fractals -- leaf design, tree shapes, etc. What this implies for algorithmic body plans.

http://en.wikipedia.org/wiki/Plant_evolutionary_developmental_biology

http://www.veritas-ucsb.org/library/origins/quotes/cambrian.html -- origin of the cambrian phyla

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http://www.veritas-ucsb.org/
http://www.veritas-ucsb.org/library/origins/quotes/cambrian.html
http://www.veritas-ucsb.org/library/origins/GRAPHICS-CAPTIONS/sub2.html

Contrary to both Darwinian gradualism and punctuated equilibria theory, the vast majority of phyla appear abruptly with low species diversity. The disparity of the higher taxa precedes the diversity of the lower taxa. --

An estimated 50 to 100 phyla appear explosively at the base of the Cambrian. Fossil evidence suggesting their common ancestry is not found in Precambrian rocks. A General Theory of Macrostasis is needed to explain the fossil data and the stability of the higher taxa.





======




http://en.wikipedia.org/wiki/Timeline_of_evolution

Diploid cells have paired chromosomes which are connected at the centromere in a typical "X" formation. Each part of the chromosome is called a chromotid.

Haploid cells have unpaired chromosomes (????)

Mitosis is binary cell division that occurs during growth (or repair) of a plant or animal. The daughter cells are identical to the mother cell.
Meiosis is sexual division in which a diploid cell divides into two haploid cells, each chromosome of which is half of the parent's chromosome pair, a sperm or an egg.




Internal Structure of Eukaryotes during cell division
There are two forms of cell division.

A mitotic spindle separates the chromosomes of a eukaryotic cell during cell division. The spindle is formed of microtubules.







The internal structure of eukaryotes ...s.


Cell Division -- Mitosis. The mitotic spindle, made up of microtubules, forms during cell division.

When cells divide a-sexually, the chromosomes appear to be pulled apart












Microtubules



Internal Structure of Eukaryotes:


The internal structure of












Microtubules



Sir Charles Lyell (1797–1875) on Evo-Devo

... Of course the science was unknown in his day, but the following observation fits right into the theory (and capsulizes my principle objection to evolution as it is usually presented).


"Lamarck enters upon the following line of argument: The more we advance in the knowledge of the different organized bodies which cover the surface of the globe, the more our embarrassment increases, to determine what ought to be regarded as a species, and still more how to limit and distinguish genera. ... The greater the abundance of natural objects assembled together, the more do we discover proofs that every thing passes by insensible shades into something else.I must here interrupt the author's argument, by observing, that no positive fact is cited to exemplify the substitution of some entirely new sense, faculty, or organ, in the room of some other suppressed as useless. All the instances adduced go only to prove that the dimensions and strength of members and the perfection of certain attributes may, in a long succession of generations, be lessened and enfeebled by disuse; or, on the contrary, be matured and augmented by active exertion. It was necessary to point out to the reader this important chasm in the chain of evidence, because he might otherwise imagine that I had merely omitted the illustrations for the sake of brevity; but the plain truth is, that there were no examples to be found; and when Lamarck talks "of the efforts of internal sentiment," "the influence of subtle fluids," and "acts of organization," as causes whereby animals and plants may acquire new organs, he substitutes names for things; and, with a disregard to the strict rules of induction, resorts to fictions, as ideal as the "plastic virtue," and other phantoms of the geologists of the middle ages. It is evident that, if some well-authenticated facts could have been adduced to establish one complete step in the process of transformation, such as the appearance, in individuals descending from a common stock, of a sense or organ entirely new, and a complete disappearance of some other enjoyed by their progenitors, time alone might then be supposed sufficient to bring about any amount of metamorphosis. The gratuitous assumption, therefore, of a point so vital to the theory of transmutation, was unpardonable on the part of its advocate."
Lyell, Principles of Geology (1850)
Ch. 35: Transmutation of Species, p. 546

Lyell's point, translated into modern terms, is even more powerful: that the only evolution that is observed in the fossil record can be expressed in terms of evolutionary development.  "Substitutions of a new sense, faculty or organ" simply does not occur. Evo-devo may produce remarkable divergences, but they develop from a common, conserved package of genes. Totally new gene packages represent a quite different and higher level of achievement, and (arguably) simply do not arise.



The Cnidaria (Coelenterata)
Phylum A-4


The Cnidaria are relatively simple animals -- they have few of the body parts of higher animals. But a defining feature of the phylum is the presence of stingers (nematocysts) used for food-gathering and other tasks. The nematocysts are complex marvels of engineering sophistication.

The Cnidaria are relatively simple animals -- they have few of the body parts of higher animals -- no enclosed digestive tract, nerve network, circulatory system, vision, skeletal structure, or appendages to aid in movement -- but they have a means of communication to coordinate actions. They are radially symmetric and digest food in an open interior sac. The phylum includes corals and jellyfish (= medusas).They are soft-bodied, but corals secrete calcium carbonates that form the hard coral reefs that house millions of individual animals. A few corals show up in the Cambrian era (520 Ma) , but become abundant about 100 My later, in the Ordovician era . The modern corals date from the Devonian era (about 240 Ma).

"The distinctiveness of cnidae, the production of which unambiguously diagnoses a cnidarian, also make them unsuitable for determining evolutionary relationships of [organisms] that otherwise seems closely related to cnidarians."
Daphne Fautin

There are a large variety of nematocysts, which may even vary geographically for the same or similar species. This implies that there is a robust evolutionary mechanism at work which supports variability around a basic gene package. I conjecture that this evolutionary variation occurs primarily in the parameters of gene expression.


The Engineering of Stingers


  The geologist Buckland once marvelled at the exquisite attention to engineering detail that is revealed in ancient fossils.

“We are almost lost in astonishment, at the microscopic attention that has been paid to the welfare of creatures, holding so low a place among the inhabitants of the ancient deep…. If there be one thing more surprising than another in the investigation of natural phenomena, it is perhaps the infinite extent and vast importance of things apparently little and insignificant.”
Buckland, regarding Crinoid fossils ibid. p.441, p.445

Our own fascination is with the Cnidarians - Phylum A-4, which includes corals and medusas. All species in this phylum are radially symmetric and have stingers, called nematocytes. The cnidarians are (relatively) immobile, and gather food with stingers which inject neuro-poisons (hypnotoxin) to immobilize their victims.

The nematocysts have been called the "most complex organelles of animal cells
[FOOTNOTE: Stefan Berking & Klaus Herrmann, Formation and dischare of nematocysts, (2005) ]." They are small -- about the size of an average bacterium (up to 60 µm in length).

nematocyst
Figure ??
Nematocyst


A cnidarian may have many thousands of these nematocysts with various specialized functions. When fully mature they appear able to function somewhat independently of the host. Some species eat cnidarians and preserve immature nematocysts (called "kleptocnidae") for their own defensive use[FOOTNOTE: "Certain types of sea slugs, such as the nudibranch aeolids, are known to undergo kleptocnidae (in addition to kleptoplasty), whereby the organisms store nematocysts of digested prey at the tips of their cerata." http://www.answers.com/topic/nematocyst].

The engineering challenges are as follows[FOOTNOTE: Following Fautin and Shimek]:

• The cell wall is super-strong, to resist extreme pressure without bursting. One scientist estimated that "the tip of the nematocyst thread is forced out of the capsule [by hydrolic pressure, although some authors assert that electrical repulsion initiates the explosion - dcb] at the astounding acceleration of 40,000g!" This is over 30 times the water pressure at the deepest part of the ocean (16,000 psi ~ 1,100 atm) and is strong enough to penetrate almost any biological structure, including shells and exoskeletons
[FOOTNOTE: Shimek, ibid.]. Despite this, water can pass through the cell wall.

• A hollow tube is tightly coiled under tension inside the cell, which leads to the question: how does the coil get packed into the cell? (An analogous packing problem exists for packing of viral dna inside its capsule). This tube is packed inside-out with barbs along the inner surface (which will be the outer surface once the tube is discharged). The venom may be stored in the tube[CHECK].

• The propulsion is provided by a concentrate of calcium ions that are stored in a water-tight sac. When the cyst is triggered, these ions rush into the cell, and immediately cause a severe osmotic imbalance  so that water rushes into the cell, swelling it rapidly to the point of explosion directed through the lid. The hollow piercing barb penetrates the victim's skin; the coiled tube passes through the tube and poison is ejected through the tip of the tube or through the tube wall.[GET REFS -- is this consistent with Fig below??]

• The activation time is the fastest in the animal kingdom: the entire process is complete in 3 ms[FOOTNOTE: Berking, ibid. Also Kurz, et. al., Mini-Collagens in Hydra Nematocytes, (1991): "The explosive discharge of cnidarian nematocysts is one of the fastest and most spectacular events in biology. High speed cinematographical analysis has shown that the whole exocytotic process takes <3 ms (Holstein and Tardent 1984)."]. Electric triggering causes the cell volume to increase by 10%, which opens the lid, and the dart ejects in a few µs, propelled by hydrostatic (osmotic) pressure."

• The triggering mechanism is generally a combination of mechanical and chemical response, so that discharge occurs when the trigger is touched by the right prey[FOOTNOTE: REF??]. Either mechanical or chemical response alone is not sufficient.[GET REF]

At present, the details of the nematocyst's life cycle are uncertain. Figure ?? summarizes one current view (expressed in general terms with some details missing). Ultimately, of course, every detail must be explained in terms of ordinary chemistry, but many questions remain.

Nematocyst Life Cycle
Figure ??
Model of the Nematocyst Life Cycle
Berking & Hermann Fig. 3  (2005)

There does not appear to be full concensus on the details of the  discharge mechanism -- how the remarkably rapic high pressure impulse is created. The wikipedia article credits "a large concentration of calcium ions"; the above references assume electrical repulsion and osmotic pressure; other discussions assume a role for spring tension in the coil. It seems fair to conclude that this is still an unsettled question.

Similarly the storage of the toxins, or how it enters the victim does not appear to be fully settled.




 

Cuvier on Fossils


"It is to fossils alone that must be attributed the birth of the theory of the earth; that, without them we could never have surmised that there were successive epochs in the formation of the globe, and a series of different operations. Indeed, they alone prove that the globe has not always had the same crust, by the certainty of the fact that they must have existed at the surface before they were buried in the depths where they are now found. It is only by analogy that we extend to primitive formations that conclusion which fossils enable us definitively to ascribe to secondary formations; and if there were only formations without fossils, no one could prove that these formations were not simultaneously produced. Again, it is to fossils, small as has been our acquaintance with them, that we owe the little knowledge we have attained respecting the nature of the revolutions of the globe. They have taught us, that the layers which comprise them have been undisturbedly deposited in a liquid; that their alterations have corresponded with those of the liquid; that their exposure was occasioned by the removal of this liquid; that these exposures have taken place more than once. None of these facts could have been decided on without these fossils."
Sir Georges Cuvier (1769-1832) Discourse on the Revolutions of the Globe (1832), p.36


Extinctions in the Fossil Record


There were a number of major extinctions of animal and plant life over the nearly 3.5 billion year fossil record.
Major extinctions:

Date
Event
Marine
Land
Cause
Remarks
450-440 Ma
Ordovician-Silurian extinction event
60% invertebrates
----
continental drift
to polar regions
2 bursts, 1 Ma apart
364 Ma
Devonian Extinction Extinction Event
Agnathan fishes,
19% familes,
50% genera
land not
affected
Asteroid or comet?
Environmental
changes?
(sea level, anoxia)

251.4 Ma
Permian-Triassic Extinction Event
"Permian-Triassic Boundary"
96% of
all species
70% of
vertebrate
species
Asteroid?
fungal plague?
Animal extinction over 10-60ky.
Plant extinction over 100-300ky.
199.6 Ma
Triassic-Jurassic Extinction Event
50% species

Asteroid?
climate change?
Volcanic activity?
within 10ky.
65.5 Ma
Cretaceous-Tertiary Extinction Event
K-T Extinction, K-T Boundary
ammonites
dinosaurs
Chicxulub Impact





In my view these extinctions were part of God's plan, and in effect "cleared the deck" for the subsequent creation.














Fossil Record of Plant Development
    All plants develop from embryos and are multi-cellular eukaryotes[FOOTNOTE: Margullis, Kingdoms and Domain, p. 413].

Phylum
Innovation
Date (Ma) of earliest fossils

Cyanobacteria (B-6) photosynthesis
nitrogen fixing
heterocysts
atp synthesis (energy storage)
sucrose cycle (Calvin cycle)
proton pump
spores (akinetes)
Spores protect the living cell by surrounding the cell with a thick wall that can resist dessication, heat, and even the vacuum of space for prolonged periods of time.
3,500 Ma


The first fossil living species were already colonial -- witness the cyanobacterial chains and the stromatolyte formations. Cells in a colony differentiated their tasks -- for example, nitrogen fixing heterocysts had to be specialized because fixing is poisoned by the oxygen byproduct of normal cell metabolism. After the invention of the eukaryotic cell, multicellular plants and animals arose. Multicellularity is caused by a delay in the process of cell separation after division.



Eukaryotic Cells
~1,500 Ma



First Multicellular Plants and Animals
~600 Ma?? (Ediacara)


Kingdom Fungi Not considered part of the plant kingdom by Lynn Margulis."fungi are clearly more closely related to animals than to lants, considering that chitin is the main component of both fungal cell walls and the arthropod exoskeleton. Plant cell walls instead contain cellulose."[FOOTNOTE: Ibid., p. 382]
~500 Ma (Ordovician)


The earliest animals appear in the fossil record before the earliest fungi and plants. A possible reason is that the early animals all developed in water environments, protected from harmful cosmic rays. Plants and fungi are basically land-based, and so could not fully develop until the cosmic rays were at least partly mitigated by the ozone layer.



Migration to Land
~470 Ma.


Migration to land faced a number of problems:
Cosmic Radiation. The atmosphere's ozone layer protects land plants and animals from most high energy cosmic and solar rays. It first became effective around 400 Ma. Some early fungi appeared at as early as 500 Ma and mosses about 470 Ma, both in the Ordovician era. Cosmic and solar radiation at this time was still severe, but for these simple plants, that was only an inconvenience, because every plant zapped by radiation became food for other plants. As long as the plants could find some shelter from direct rays (overhangs, soil, depressions, water) and their reproduction could keep ahead of the destruction, they were able to cope.
Dessication. A more serious problem for migration to dry land was the need for water. This limited the earliest land plants to moist environments.
Structural Support. A water environment provides  considerable support for weighty bodies, but when plants grew into the atmosphere, they had to support their own weight. Thus early land plants were limited to low-rising masses.




Vascular Plants.
~450 Ma


Club Mosses,
Lycopods  (PL-4)
At one time were very prolific -- heights to 40m in the carboniferous age (350-290 Ma). No true root -- grow from rhizomes as do some of the non-vascular plants  (mosses, etc.)
400 Ma. Carboniferous


Horsetails (PL-6)
Prolific in carboniferous age  -- heights to 15m.



Ferns (PL-7)
Prolific in carboniferous age  -- heights to 25m. Require moist environment for fertilization.




dessication resistance This innovation was needed before plants could thrive in a dry atmosphere. Major innovations involved:
     • Pollen Tube. This allows fertilization in a dry environment[FOOTNOTE. ibid., p. 419]. From the Gincko (Pl-9) and later.
     • Leaves (flat areas for chlorophyll) originated in the Devonian Era (around 400 Ma).
     • Cutin -- a waxy layer to retain moisture in all plant surfaces that exist in an air environment (such as leaves and stems); and
     • Stomata -- pores in the leaves that can open or close to control respiration.
"Leaves did not become widespread in fossil floras until 50 million years after the emergence of vascular plants." ref (Devonian around 400 Ma)




Early Seed Plants (Lyginopterids) in Devonian
380 Ma


Land Plants appear in the Middle Silurian - about 420 Ma. The first true seeds about 380 Ma.


see: "Greening of the Land" Chapter XXIII of Rich, The Fossil Book



root system

vascular structures
     • Cellulose
     • Phloem
     • Xylem 
     • Woody tissues

(425Ma) Cooksonia


cell wall/woody structures




gametes/sexual reproduction




gymnosperms




angiosperms (flowering plants)



Bryophytes non-vascular plants (algae)



Tracheophytes
vascular plants (algae)











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REFERENCES

David C. Bossard, Abundant Life: The Diversity of Life in the Biosphere, IBRI Colloquium lecture (2001). PDF versions: text, slides.
David C. Bossard, The Chemical buildingblocks of Life. IBRI Colloquium lecture (2001)
David C. Bossard, Geology Before Darwin: The Struggle to Find and Defend the Truth about the Earth’s Past IBRI Colloquium lecture (2003)
David C. Bossard, A Fit Place to Live: Creation of the Biosphere IBRI Colloquium lecture (2003)
David C. Bossard, The Stones Cry Out: How Early Christian Geologists Enlarged their Understanding of the Creation Account IBRI Colloquium lecture (2006)
Daphne Gail Fautin Structural Diversity, Systematics, and Evolution of Cnidae, Elsevier, (2009)
S.M.Gon, Pictorial Guide to the Orders of Trilobites
Stephen Jay Gould, Wonderful Life: The Burgess Shall and the Nature of History (1989).
Nigel C. Hughes, Trilobite Construction: Building a Bridge across the Micro- and Macroevolutionary Divide, (2005) In my view this article follows classic evolutionary reasoning in contrast to the approach implied by evo-devo.
Lynn Margulis, Kingdoms and Domains, An Illustrated Guide to the Phyla of Life on Earth, 4th edition (2009)
Riccardo Levi-Setti, Trilobites, (1993).
Patricia & Thomas Rich, Mildred & Carroll Fenton, The Fossil Book: A Record of Prehistoric Life, Dover, (1996), Chapter XXIII p. 372ff; XXXII, p. 534ff).
J. William Schopf, Cradle of Life: The Discovery of Earth's Earliest Fossils (1999).
Colin Tudge, The Variety of Life, Oxford, 2000.
Hou Xian Guang, Richard J. Aldridge, et. al. The Cambrian Fossils of Chengjiang, China. Blackwell, (2007).

Wikipedia Articles:  Animals (Describes the various animal phyla,


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Prepared July, 2010