Monday, April 23, 2007

ID vs ERVs-- Part Eight: Black Hole Swallows Planet of the Straw Men

A continuation of Part Six and Seven.

What follows are the most absurd arguments against evolution I have heard in my entire life. Mr. Black Hole has set up an entire planets worth of 'Darwinist' straw men for himself, and whoooo boy! Hes takin' a battle axe to the poor creatures! But before you burn your eyes reading his powerful refutations of Evilution, let me list the sacrificial straw men:

(a) functional units in the genome consist solely of protein-coding loci ("genes"*) and their associated regulatory regions, with a few exceptions;

(b) all inherited, important aspects of the phenotype are specified by proteins and some RNAs;

(c) the "Central Dogma" holds;

(d) the mapping relation that exists between genotype and phenotype is that of programming instructions (DNA) and the programmed output (phenotype);

(e) genes act and evolve in an independent manner at the DNA level;

(f) higher-order structures such as chromosomes and cells are passive with respect to form-generation, the active agents being genes; and

(g) DNA sequences evolve by a combination of neutral forces and selection pressures.
Not to be a first grade teacher here, but how many of these straw men can you all kill off the tops of your heads? Who is Mr. Black Hole trying to kid with "This is what evilutionists believe!"?

Since ID Creationists love analogies, I also find it interesting that ID Creationists like to alternate degrading the intelligence of their followers with flattery ("Heck even I know how to refute E! Im so smart! Evilutionists are so dumb!"). Just seems familiar, thats all.

So thats your argument, Mr. Black Hole?

siRNA can regulate gene function, and siRNA isnt necessarily in a 'flanking region', therefore Straw-Man-A is dead, therefore evilution is false, therefore your creation myth is true?

Epigenetics exists, 'therefore Straw-Man-B and F are dead, therefore evilution is false, therefore your creation myth is true?

Retroviruses exist, therefore Straw-Man-C is dead, therefore evilution is false, therefore your creation myth is true?

Theres not one gene for 'red hair' or 'good at sports', therefore Straw-Man-D is dead, therefore evilution is false, therefore your creation myth is true?

Genetic linkage exists, therefore Straw-Man-E is dead, therefore evilution is false, therefore your creation myth is true?

Straw-Man-G is gobbldy gook, therefore Straw-Man-G is dead, therefore evilution is false, therefore your creation myth is true? (If anyone can translate Straw-Man-F for me, Id appreciate it)

Thats his logic.

You think Im being simple? Surely this isnt really his argument, right? Shield the eyes of near-by children, readers:

(1) Functional units in the genome do not consist solely of protein-coding loci and their flanking control regions. Instead, functional units of the genome comprise a host of different DNA classes, for example, loci for regulatory RNAs, centromeres, nuclear matrix attachment sites, chromatin boundary elements, transcriptional control sites, and exons, to name but a very few. REs are known to consist of concatenations of functional, nonprotein-coding regions as well as protein/RNA-coding domains. Many cis-regulatory sequences are recognized to be repetitive in that multiple copies of the element are dispersed throughout a genome.

(2) Inherited aspects of the phenotype are specified by more than proteins and RNAs. Following point 1, nonprotein-coding DNA regions have been shown to have an array of direct and indirect phenotypic effects, in addition to providing the systems architecture for protein-coding loci.

(3) The Central Dogma is incomplete. Facets of the Central Dogma are now being seriously questioned, especially since it has been determined that chromatin conformations and cytoplasmic states can be meiotically inherited, a single "gene" can code for many different proteins**, cells can detect and modify exogenous DNA***, and metabolic conditions can (de)activate or modulate a range of mutational processes. Proteins can even impose function on otherwise "functionless" DNA sequences—such as the emergence of neocentromeres from noncentromeric DNA regions. In addition, multiple functions can be layered onto a single DNA segment. Information flow in the cell is hardly the linear specification chain imagined in the 1960s through the 1990s.

(4) A multi-layered mapping relation exists between genotype and phenotype. Cause and effect in phenotype specification are becoming increasingly difficult to discern. The connection between genotype and phenotype is a many-to-one and one-to-many network of mappings, all of which are context-dependent.

(5) Although many alleles do show Mendelian inheritance, genes do not act and evolve in an independent manner. DNA activity and mutational alteration are embedded in the context of chromatin domains, the chromosome, nuclear compartments, the cell, and epigenesis. There is no such thing as autonomous DNA unit action or evolution.

(6) No justification can be provided for ascribing greater ontological significance to one set of cellular components (e.g., protein-coding regions) over another (e.g., the cytoskeleton). Indeed the line between the "genome" and the "encoded cell" has blurred. The fact that ciliates literally engineer their "somatic" chromosomes, and phenomena like RNA editing and position-effect phenomena, readily gives the lie to the notion of DNA being the sole active, "directing agent" in the cell.

(7) DNA sequences change by more than a combination of neutral forces and selection pressures. Models of DNA sequence evolution that recognize only neutral and selection-driven genomic changes persist in biology textbooks, phylogenetic models, and population genetics, but these are now seriously outdated. Many routes of genomic alteration, even point mutations, are actually or potentially under some form of metabolic control. There thus appears to be a spectrum of "mutational control" in the cell, ranging from the strictly targeted (site-specific) to the "random," operating at a stage before screening by natural selection or genetic drift.
.... Ta dah?

Readers, I expect you all to mail me boxes of wine (BOXES, not bottles) for reading this crap. I need it. To use my favorite descriptor, this paper is like a coagulated word salad:
What all of this means is that the postulates of the genome model supporting the selfish DNA narrative are either false or need to be modified out of recognition. The genome definition based on points 1–7 goes beyond simply DNA ≠ genome; it rather indicates that DNA genome, and quite possibly (DNA + chromatin proteins) genome. If we want to maintain the metaphor of a book, then the genome is an interactive, semiotic, and super-sophisticated text that has, at this time, no other physical counterpart. It is a genomic book where, for instance, a sentence can take on a hundred related but different meanings, depending on the epigenetic context, all of which are compatible with the whole text. Furthermore, the genome-book contains many cryptic writings that, when transposed, rearranged, or read with an epigenetic decoder, reveal their meanings.


* Yeah, he puts "gene" in quotes through the entire paper. Creationists dont believe in "genes", evidently.
** Once again, Mr. Black Hole is convinced HIV operates through magic.
*** Okay, you know that 'Fundies Say the Darndest Things' where a Creationist almost discovers the sun? Mr. Black Hole, a biologist (**WINK!!!**) has just discovered restriction enzymes. EcoRI exists, therefore Creationism is true. ROFL!!! I hurt myself laughing so hard at this one!

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