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In the book "Why Evolution Is True" the author states:

--- it really consists of six components: evolution, gradualism, speciation, common ancestry, natural selection, and nonselective mechanisms of evolutionary change. (p-3)[emphasis supplied].

This blog argues that the materialistic interpretation of the species-to-species common ancestor concept, and its origins implications, is refuted by data related to the origin and development of animal body plans.



MODULE SUBJECTS

BODY PLAN MECHANISM: PLAUSIBILITY (Click Here For Summary)

BODY PLAN MECHANISM: ORIGIN (Click Here For Summary)

THERAPSIDA: A GEOGRAPHICALLY ISOLATED POLYTOMY (Click Here For Summary)

SYNAPSID PHYLOGENY: IMPLAUSIBLE GHOST SPECIES (Click Here For Summary)

HORIZONTAL GENE TRANSFER (Click Here For Summary)

GENETIC TOOLKIT (Click Here For Summary)

GENE REGULATORY NETWORK (Click Here For Summary)

PELYCOSAURS: SPECIES SPLITTING PARADOXES (Click Here For Summary)

BODY PLAN MECHANISM: PLAUSIBILITY
(updated 07Nov14)

1. Body plan morphology and phylogeny imply the action of a guidance mechanism.

2. Dynamic Patterning Modules are perceived as the mechanism.

3. Dynamic Patterning Modules:

---are a subset of genes in the developmental-genetic toolkit;

---are perceived as a pattern language;

---control the development of all metazoan body plans;

---considered to be the distinguishing properties of multicellular life;

---are regulatory networks that function as self-ordered properties;

---constitute body plan self-organization;

---first appeared during the Proterozoic Eon (2500 Ma to 542.0±1.0 Ma (million years ago), before the appearance of bilaterian animals;

---control clustering capabilities that emerged in pre-existing cell surface molecules;

---pre-existed multicellularity;

---are/were physically inevitable;

---are an example of Orthogenesis that assume a limited set of characteristic forms;

Guidance mechanisms are inferred based on a range of observed conditions of body-plan development, organization, and controls that the reality of the concept can be objectively argued as a plausible mechanism.
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BODY PLAN MECHANISM: ORIGIN
(updated 01Dec14)

The nature of unknowns concerning the origin and assembly of phylum-level organism body-plans include:

---lack of a definitive organism origin in which the first body plan was assembled;

---conflicting hypotheses involving phylogenetic path of body-plan development;

---the completeness of body plans at their first appearance;

---the seeming tendency of body plans to follow an ordered developmental sequence;

---the apparent trend toward limited final body-plan configuration;

---the unidentified causative agent in the appearance of novel phylum-level traits.

These unknowns have resulted in the implication that the origin, assembly, and form of phylum-level body-plans operate under the control of a pre-existing guiding mechanism---the field provides no objective evidence to refute the argument that the controlling templates appeared long before the appearance of body plans and thus the template designs were not influenced by those physical body plan properties.
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SYNAPSID PHYLOGENY: IMPLAUSIBLE GHOST SPECIES

(updated 17Feb15) The foregoing cladistic methodology and conventional understanding of body plan relationships is thus summarized:

---The body plans of most fossils indicate that species first appear with a complete complement of body plan traits sufficient to establish taxonomic identity.

---Those species specific complements of body plan traits are essentially unchanged at a species last appearance in the fossil record.

---Cladistic methodology views sister species whose body plan complements are sufficiently different to require their different taxonomic classification.

---Cladistic methodology views ghost species body plan as being different sister species.

---Cladistic methodology views asynchronous appearance of sister species represents the presence of an unidentified ghost species as the precursor of the later appearing species.

---Stratigraphic organization of inferred cladogram phylogenies establishes the reality of widespread asynchronous species first appearances whose body plans have no documented body plan precursor.

---Since Cladistic analysis inadvertently confirms the conventional view that taxa appear whose fully developed body plans have no discernible body plan association with a precursor species body plan, it cannot be rationally denied that the taxa in Figure 2 acquired their body plans from some source other than a common ancestor, and thus were pre-designed suggesting an organizing template that arose independently from body plan origin materialism, as argued in the "ORIGIN" module.
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THERAPSIDA: A GEOGRAPHICALLY ISOLATED POLYTOMY
(updated 4Jan15)

The conditions associated with this therapsid polytomy include:

---a similar body plan was present in all of the lineages at their initial appearance;

---the similar body plan was present in the lineages in separated land masses;

---the body plan appeared in the absence of immediate lineage body plans;

---the body plan consisted of phylum level characteristics that first appeared 200 million years before they appeared in the therapsids;

thus: the simultaneous appearance of taxonomically identical lineages on separate continental plates with phylum level characteristics that first appeared 200 million years earlier during the Cambrian, indicates a guiding mechanism whose body patterning processes were available for application before the lineage's body plans began their assembly, a mechanism referred to as a patterning template in the "ORIGINS" module.
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PELYCOSAURS: SPECIES SPLITTING PARADOXES
(updated 16Jan15)

---Cladistically determined pelycosaur phylogenies produce simultaneously appearing sister species due to species splitting at clad nodes.

---Sister species are so named due to their body-plan commonality patterned after the body plan of the common ancestor living at a clade node, after which the ancestor dies and the body plan is no longed available to influence further species development.

---All of the sister species documented in the cladogram referenced in this module exhibited sufficient temporal differences in their first appearances to preclude their simultaneous development at a single clade node.

All of the sister species documented in the cladogram referenced in this module exhibited body-plan traits and assemble processes that required a common mechanism, exhibiting the characteristics of a patterning process that was in effect before the first and subsequent pelycosaur species-level body plans developed.
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HOX GENES
(undated 27Dec14)

The current understanding of Hox gene cluster origin and subsequent development is conveyed in part with illustrations of the coordinated relationship between Hox cluster gene complement and associated phylogenetic structures which suggests the following:

---The disassociation between the appearance of Hox clusters capable of controlling body part positioning and the appearance of organisms with body parts they were destined to control implies that the Hox cluster controlling processes were programmed.

---Inferred Hox cluster duplications produced new clusters, and associated genes, whose new body part positioning processes were integrated with pre-duplication positioning process to achieve an overall body part position system that implies a programmed control.

---The ultimate achievement of phylum level body part control through numerous duplication events that incorporated new gene processes into the accumulating Hox cluster complement implies a pre-existing guiding program.

The several conditions between the appearance of successive Hox cluster body part control capabilities and the ultimate application of those capabilities to later appearing body plans implies they were programmed by a pre-existing patterning mechanism.
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GENE REGULATORY NETWORK
(updated 18Dec14)

Gene Regulatory Networks:

---Are considered to control the development of both complete body plans and their constituted parts;

---achieve these ends through the control of cellular biochemical sequences whose final products are proteins;

---biochemical sequences are controlled by processes that determine the relative positioning of cells;

---mathematical models are the means to describe and mimic the biochemical sequences and cellular positioning;

---positioning, when viewed in relation to morphological realism, includes the size, shape, and relative arrangement of individual and collective body parts in coordinated sequences, each sequential part programmed to achieve a final part.

The models do not have the capability to generate facsimiles of the size, shape, and relative arrangement of individual and collective body parts, either in embryological development or in the appearance sequence of major body part innovations, but they exhibit the characteristics of coordinated organization of the biochemical sequences to achieve a final protein, a process that reflects the guidance by an organizing mechanism, referred to as a template in the "BODY PLAN MECHANISM: ORIGIN:"module.
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GENETIC TOOLKIT
(updated 25Nov14)

---Genetic/molecular components are the fundamental operational processes of the Developmental Genetic Toolkit.

---The fundamental genetic/molecular components made their initial appearance in unicellular animals and thus were in place at the advent of multicellular animals.

---Subsequent duplication of the toolkit's genetic/molecular components added to, but have not altered, these genetic/molecular processes.

The apparent duplications in the components that comprise Gene Regulatory Networks and Hox gene clusters , the mechanisms that actually control the origin, assembly and patterning of animal phylum-level body plans, essentially makes the toolkit concept irrelevant as an important factor in body plan development..
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HORIZONTAL GENE TRANSFER
(updated 08Nov14)

Irrespective of where in a descendant organism's phylogenetic development a Horizontal Gene Transfer from other organisms occurred, and irrespective of the magnitude of the transfer, the descendant organism's genetic complement includes the ancestor's Horizontal Gene Transfer complement and thus the two organisms do not represent a common ancestor sequence but, in combination of lineage branching, represent a web of Horizontal Gene Transfers and thus there is no organismal tree and no most recent "body-Plan" common ancestor nor Last Universal Common Ancestor in terms of species-to-species lineage.
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