I found Daniel’s rebuttal to my endogenous retrovirus argument quite thorough, as was the rest of his post. Entailed here is my response to his latest exposition.

The ET Hypothesis

It is entirely irrelevant whether or not particular proponents of intelligent design have religious motivations behind them; the theory of intelligent design merely holds that certain biological features on earth are better explained by rational action that purely undirected processes.
To argue that the proponents of intelligent design are religiously motivated, and that, therefore, intelligent design holds that God is the designer, is as fallacious as me arguing that social Darwinism is the very epitome of the Neo-Darwinian narrative.

The reason why I so passionately argue against the notion that the intelligent design proposition holds that the designer is God is because this is simply untrue.

Design As An Explanation
Perhaps I was not entirely clear in my exposition on how the theory of intelligent design works.
As I stated earlier in one of my posts, the theory of intelligent design holds that certain features of the universe and biosphere are better explained by the actions of a rational agent than purely undirected processes.

Now, I have this proposition; and that is that it is implausible that certain protein primary structures can arise through Darwinian mechanisms of natural selection and random mutations in the gene pool. I know of no undirected evolutionary mechanism (like Lamarckism or saltationism) which can offer a feasible model that would demonstrate how these protein primary structures arose.

However, directed enzyme evolution techniques, i.e. intelligent design, can engineer these proteins; I therefore conclude that intelligent design through directed enzyme evolution is a far more rational explanation for certain protein primary structures than the Darwinian synthesis.
In short,
1) Darwinism has no explanation for X,
2) Intelligent design does offer a mechanism for X,
3) Therefore the intelligent design postulate is a more adequate explanation for X.

I fail to see any flaw in my logic and rational.
To summarize,
· What is the origin of the genetic code? Ribosomal engineering techniques explain the origin of the genetic code better than undirected processes.
· What is the origin of the homochirality of amino acids used by life? What’s the problem with a designer using chiral synthesis pools and chemical bonding breakage technology?
· How could "longer and more complex proteins (for example, those belonging to the alpha/beta classes)" arise? Directed enzyme evolution coupled with recombinant DNA techniques.
· What is the origin of the complex metabolic pathways involving glycolysis? Metabolic engineering dunnit.
· Why do some viruses use RNA, some use single strand DNA, and some use double strand DNA for their heritable material? Degenerative processes dunnit.
· Why is this protein or this system or this anatomical part used instead of this other one? I don’t get the point of this argument or any of the arguments entailed below this one.

A Case Of Bad Probabilities?

I concede the point that my argument on enodenous retroviruses and probability has been successfully refuted; nevertheless, I believe I can demonstrate that my argument on protein evolution and probability does indeed indicate that there is indeed virtually no chance of protein primary structures evolving through Darwinian mechanisms.
The fact here is this:
That there is, au grand sérieux, an ultimate goal in protein evolution – and indeed in all evolution. And that goal is (beneficial) functionality. Thus, in protein evolution and in morphological evolution, and all organic change, there is a goal. Since there is a goal, it is extremely improbable for certain protein primary structures to evolve through Darwinian mechanisms.
To put this in the form of card-playing:
Let the royal flush be functionality, and all other card sequences redundant, non-coding regions of DNA. What is the probability of the royal flush being obtained? Next to nil, and this is analogous to my argument on protein formation.

Amino Acids And The Genetic Code
Throughout this debate, my central argument is not merely ‘mainstream science has not explanation for X, therefore goddunnit.’ My argument is based upon a clear and conscience acknowledgement of the fact that the intelligent design postulate does not hold that intelligent design is absolutely necessary for the origin of life or its ultimate diversification, but rather that certain features of the biosphere are more adequately explained by the intelligent design proposition.
I believe this is precisely the case regarding amino acids and the genetic code.
In the case of homochirality, the Darwinian synthesis offers no explanation for the origin of this peculiar feature of the biological world, whilst intelligent design does offer a plausible hypothesis for the origin of homochirality. That hypothesis is not and never has been ‘intelligent designer dunnit, next problem’. The plausible mechanism for the origin of homochirality is that of asymmetric synthesis and chiral synthesis pools. In short, a chiral substance would be manipulated through a series of biochemical reactions employing achiral chemicals to eventually obtain the wanted chiral molecule, i.e. the chiral molecule desired would be ‘purified’ from a pool of molecules consisting of both enantiomers.
This would offer a brilliant and plausible explanation for the origin of homochirality using an intelligent agent. This would effortlessly explain such an origin, while the Darwinian synthesis offers no possible mechanisms.




The Case Of Nylonase

I do not believe that the evolution of nylonase is a case against my argument on protein evolution.
While I do not know the exact mechanism (Daniel said it wasn’t a frameshift mutation or gene duplication actually), I can postulate this: that in the case of EPSP synthase, there is a ‘barrier’ as it were of non-coding nucleotide primary structures; however, I hypothesize that in the case of nylonase, there is no such barrier, and any mutation occuring at that particular chromosomal loci will result in beneficial functionality. Again, I fail to realize how this applies directly to this conversation on protein evolution.

Answering Critiques Of My Previous Post

On the nylon bug and my statement that ‘the ability was already present,’ I regret I did not clarify that statement; in detail, I mean this: the ability to synthesize nylon, i.e. the potential to do so, was present. The potential to evolve the functionality of synthesizing nylon was already present, as it did not require natural selection to ‘browse’ through an endless array of non-beneficial protein primary structures.

As to intelligent design being over at roughly 200,000 years ago:

200,000 years ago homo sapiens appeared on earth. I hold that homo sapiens was the last act of design the intelligent designer did. Why do I hold to such a proposition?
There is a linear curve imposed upon phylogeny; that curve, seldom negated in any way shows a definite progression of more unintelligent animals to a more intelligent class of animal. Humans are the most intelligent; the first products that evolution is supposed to have produced are the least intelligent. It seems natural to me to presuppose that the ‘wonder and glory of the universe’ (Darwin, “The Descent of Man,”), and the most intelligent of all organisms, mankind, would be the last species engineered by the intelligent designer.
As to whether the intelligent designer is at work today: I suppose it’s possible the intelligent designer is still designing things on earth, however we lack substantial evidence to support that view. If one were to find plasmids containing insert DNA of zebras for example in the genome of wasps it would be logical to assume an intelligent designer is at work here.

Now on to these hypothetical alien engineers:
As to a heritable system and a system to construct proteins, there are means and ways to get around such obstacles, albeit hypothetically. Prions for example, are suspected to not need a way to store heritable traits. This would immediately bypass the problem of these aliens needing a genetic code of sorts.

I concede the point, that, using Zipf’s laws, DNA is a language.

In Brief
In brief, I believe that intelligent design still explains the origin of homochirality and protein primary structures better than any other known synthesis which does not have intelligence.

-Livingstone M.