Saturday, May 26, 2007

ID vs ERVs-- Part Thirteen: Lets Cut to the Chase

Ive been putting off finishing the Sternberg paper because, well, I havent been feeling so hot lately, and Mr. Black Holes post-modern crap-fest doenst help with the nausea so much. I mean seriously, look at how he tries to 'disprove' transposable elements impact on 'macroevolution' (note: hes pulling all of this out of his ass. None of this is actually scientific, hes not talking above you, its po-mo.)

Consider now a developmental "selector gene" locus with an organization similar to that of the β-globin locus. Our not-so-hypothetical locus is a functional composition of various cis-acting (I, R, M, E, S, and P) and protein-coding sequences (G). So our developmental locus can be formally defined as: Locus = (I, R, M, E, S, and P) Now there must exist a morphogenetic rule, f, that maps from "genome space" (the set of genotypes) to "phenotype space" (set of morphologies) the information contained in the locus, with the phenotype being designated here as Φ. Alternative ways of expressing this relation are:

f: (I, R, M, E, S, P, G)--> Φ or
f((I, R, M, E, S, P, G)) = Φ

Let Locus now be subjected to the insertion of a TE unit (Locus-TE). This means that the following mutational event has occurred:

(I, R, M, E, S, P, G)--TE-->(I, R, M, TE, E, S, P, G)

For the TE to have a phenotypic effect, one of two things appears to be necessary. Either the set of morphogenetic rules F interpret Locus-TE in a way such that a different point in phenotype space is accessed, say Φ' instead of Φ, or F cannot interpret Locus-TE, and an entirely different phentotype is attained by default. What is crucial to note now is that the TE insertion can only act as the material cause of the phenotype shift, whereas F is the set of efficient causes generating an effect (phenotype shift), the effect itself being constrained by the structure of phenotype space, with the latter entailing formal (causes) rules of morphology. In other words, TEs can only affect how morphogenetic rules interpret genomic data; these sequences cannot, of themselves, "write" new morphogenetic rules or restructure phenotype space. Genomic turnover due to TEs and other REs can provide new data/information for the system of Fs to interpret and use, but the important causal basis of differences in body plans resides in the formal rules that structure phenotype space.


Look, this is the exact same argument as we got from the know-nothing YEC author at AiG. The whole premise of Mr. Black Holes paper is that mobile elements are integral, so mobile elements utilized by an organism are evidence of Design, but mobile elements cant 'write new morphogenetic rules or restructure phenotype space', so Evilution is false. Again, heads ID wins, tails Evilution loses.

But remember, folks, its Evilution thats unfalsifiable.

Mr. Black Hole insists that his hypothesis is falsifiable. You see, if we can just make/find an organism without any mobile elements in it, then we've proved him wrong!
One potential falsification of the integral function framework would be the construction of an artificial eukaryotic genome that lacked any form of REs and that, nonetheless, maintained all normal genomic/epigenetic functions. For example, ablating all REs from a complete set of Takifugu chromosomes, placing this diploid nuclear complement in an anucleated Takifugu zygote, and then observing normal Takifugu ontogeny would effectively negate any global functional roles of REs.
This is not a falsifiable statement. Asking for an organism without mobile elements is like asking for an organism not made of DNA-- Not because it is essential for all forms of life, but because thats how life evolved on this planet, our only source of 'life' samples at this point.
The very beginning-- the very root/net/swamp base of the Tree of Life is a mess of mobile elements and pirate DNA, thus the prediction from evolution would be that there are no organisms on this planet free of them.
Additionally, the puffer-fish has been evolving with its mobile elements for >millions of years. Why would you think you could just pop stuff out of their (or any modern) genome and everything would be hunky dory??
Oh, well I guess we always have the option of building an organism from scratch.

Ugh. Lets finish this crap.
Given all that we know of REs, the selfish DNA narrative may explain aspects of the origin of these sequences, but it certainly fails to capture the diverse roles of these elements in chromosomes and during ontogenesis.
The 'retroviruses' that created our HERVs are all dead. There are no infectious counter-parts. So ERVs are the ultimate selfish DNA-- they are retroviruses that have found a way to 'survive' where their counterparts have failed. The insertions were co-opted as needed with no original intent, which perfectly explains the diverse roles of mobile elements.

Not only that, but the selfish DNA narrative appears to be refractory to any type of falsification. Inferred evolutionary effects of REs also appear to be just-so stories.

As unpalatable as this may be for most readers, it would seem that the selfish DNA narrative and allied frameworks must join the other "icons" of neo-Darwinian evolutionary theory that, despite their variance with empirical evidence, nevertheless persist in the literature.
Oh 'icons of evolution.' How cute.


The Factician said...

You may be happy to hear that the Boeke lab at Johns Hopkins (I think he's there, don't quote me on that) is actually engineering S. cerevisiae to remove every single mobile element in the chromosome. (Though not to test that particular hypothesis). They're also doing a bunch of other massive engineering steps (like removing several redundant codons so that they can put in synthetic codons for synthetic amino acids), but I know that removing the transposons was a big part of it.

So in a few years, he'll have his pet hypothesis tested. I can't quite understand how some transposons having a function for the host kills evolution, but then again, I'm not a luminary in the ID field ;)


ERV said...

Hmm I wonder what theyre trying to do with that? I really wouldnt imagine an organism to be able to survive without its mobile elements.

Ill keep an eye out for their papers!

Anonymous said...

You're right about the Boeke lab...they're pretty much making every conceivable alteration to the S. cerevisiae genome. When they're done, there won't be much work for the rest of us. There's always drywall, I guess!
And I don't get the ID spin on this one way or the other.