Livingstone's Third Post

Before I begin, I would like to say that I will write the word ‘Clark’ one hundred times on a piece of paper for future reference ;-)
My responses will be articulated in the following format:

1. The ET Hypothesis
2. Tools of the Intelligent Designer
3. The Case of Nylonase
4. The Known, The Unknown, And The Known Again
5. Answering Andrew’s Question
6. Amino Acids
7. The Genetic Code
8. Protein Primary Structure And Utility
9. Proteins And Probability
10. In Brief

The ET Hypothesis

Intelligent Design holds that the designer is not known; this is because, while the existence of digital, semantic, linear codes is evidence for intelligent design, such a described evidence cannot indicate whether it was a ‘god’ or some other intelligence.

How then can we say that the designer is God?
The reason we assure others that intelligent design has nothing to do with religion or gods is simply because that is the truth.

The hypothetical alien-engineers could plausibly arise through Darwinian mechanisms on another planet; however, the evidence indicates that biochemical structures and life on earth is designed through intelligence.

Tools Of The Intelligent Designer

My opponent, Theo (yes I’m shortening it =D), states that the intelligent design proponents should postulate some plausible mechanism the designer used to design life on earth.
I propose one of genetic engineering for the design of protein primary structures, and a model of directed enzyme evolution for other biochemical structures.
I will elaborate on the former, but not on the latter unless my opponent wishes me to do so.

In the genetic engineering model, the designer used recombinatorial DNA and cloning techniques which we humans mirror today.
This does leave a trace, and it is called the genetic code. Perhaps this is why the genetic code is one of the strongest arguments for intelligent design.

If there were no genetic code which we could manipulate, then it would be rather hard to find a mechanism the designer may have used.
As it turns out, a model of either genetic engineering or directed evolution answers some questions the Darwinian theory cannot (I will elaborate on this in a later portion of my treatise).

The Case Of Nylonase

I really don’t know what my opponent’s reason was for bringing up the evolution of nylonase.
In the bacterium there are three enzymes, EIII (NylC) EI (NylA), and EII (NylB), which are used to digest nylon; a substitution mutation/point mutation occurred in the carboxylesterase gene which allowed the bacterium to hydrolyze nylon oligomers. The ability was already present; it simply took a point mutation to cause an alteration in the parent enzymes specificity.

The intelligent design camp is not at all surprised at this; merely one mutation was needed to achieve this function. It would be much more of a surprise to the intelligent design proponents if something that took trillions upon trillions of mutations to eventually evolve a novel function.

Nobody is denying mutations; intelligent design is over and was over about 200,000 years ago.

The Known, The Unknown, And The Known Again
I suspect that my opponent believes I am making an anthology of arguments from ignorance; I believe this will turn out to be untrue. I do not believe I am making an argument from ignorance, where we do not know of a Darwinian mechanism for X, therefore ‘an intelligent designer dunnit.’

Let me explain by first defining the intelligent design proposition:

“The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.”

I believe the fallacy in my opponent’s reasoning is the false assumption that we do not postulate any mechanism for the generation of protein structures, etc.

Intelligent design does explain the origin of protein structures better than an undirected process like the Darwinian hypothesis, and I will explain how this can be the case.

While staunch Darwinians have virtually no mechanism for the origin of highly integrated protein structures and functions, the intelligent design proposition does offer a mechanism, and one based on the scientific method.
All observations in the physical world demonstrates that complex biocatalytic functions are only a derivative of intelligence rather than undirected processes.
The mechanism the designer used is directed evolution, rather than the Darwinian mechanism.

The difference between the Darwinian mechanism and the mechanism I postulate (i.e. directed enzyme evolution techniques), are as follows:
1. Darwinism does not work towards any direction, and there is no goal.
2. A directed molecular evolution paradigm, on the other hand, has a defined goal, and processes like mutation, recombination, and selection are controlled by the designer.
Rational design explains the origin of complex enzymatic functions far better than Darwinism, and for this reason Occam’s razor cannot apply to this scenario.

There IS a mechanism for the design of proteins and ezymes, and one that is entirely testable, repeatable, and observable. The only difference is in who the designer is. In today’s world, the designer is humanity. 4.55 billion years ago, the designer could have been an alien agent or some other designer. However, the mechanism remains the same.

So as one can see, while intelligent design offers a very plausible mechanism, the staunch Darwinians are left with nothing observable or repeatable.

Answering Andrew’s Question
Here I will briefly answer the question Andrew presented: whether the ‘other factors’ I mentioned had anything to do with the anthropic principle.

In short, it so happens my training is in biochemistry and not physics, so the other factors I had in mind did not include the anthropic principle, but rather biochemical factors such as topoisomerase evolution or the fact that various papers in scientific literature are questioning the endosymbiotic hypothesis.

Amino Acids

I hold that my argument is an example of this type of reasoning, and not an argument from ignorance: (1) The Darwinian synthesis cannot explain how X could have happened, (2) The intelligent design paradigm can explain a plausible mechanism, (3) Therefore the intelligent design model best explains X.

Again, I propose yet another mechanism for the origin of homochirality, one of RNA-directed amino acid homochirality.

Again, I can elaborate on this in depth if requested to do so.

I would like my opponent to demonstrate one type of chemical reaction which spontaneously produces only one entantiomer.

Theo presents a very interesting process for the origin of homochirality; however, there is an error in this hypothesis.

This hypothetical RNA helix that is ‘swimming’ through this mixture of chemicals and amino acid residues does not select for only one entantiomer. Unless my opponent can provide peer-reviewed literature supporting the claim that RNA can only bind to L amino acids, and not D amino acids, in a free solution, I believe his hypothesis is wrong.
I am not aware that RNA would discriminate one entantiomer from another in a free solution.

The Genetic Code

This is not an argument from ignorance. This is an argument which rests upon experimental verification and observational manifestations; therefore, intelligent design explains the origin of DNA and the central dogma of molecular biology better than the Darwinian synthesis.
In the first place, DNA is obviously a language, or a code as it were. Of course, you might protest that this begs the question, whether DNA is actually a language. However, I think my position is stronger in saying that it is, as DNA follows laws of linguistics such as those postulated by Zipf.
Observation tells us that all languages are a derivative of intelligence; there is no known unintelligent process that will make a language. Therefore, I hold that intelligent design explains the origin of DNA better than Darwinian mechanisms.

RNA may have been a precursor to DNA and fully-functional replicating systems; however, we must wonder how switch gates and logic nodes which are found in the central dogma of molecular biology could evolve, as natural selection would have to select for potential biosystem through selecting at the time of the formation of 3’5’ phosphodiester bonds in RNA and DNA sequences.


Protein Primary Structure And Utility

While exaptation is an interesting hypothesis, there are several errors with it.

The case of nylonase is entirely different than the case of the evolution of EPSP synthase. Only a few mutations were needed to evolve the function of nylonase. However, as in the paper I presented, there would have to be a massive amount of mutations for the evolution of EPSP synthase.
That EPSP synthase had a different function before is largely irrelevant to the discussion; the function is not what matters, it is the (beneficial) functionally-redundant primary structures separating EPSP synthase from shorter protein primary structures.
I am not aware the EPSP synthase’s many molecular functions are vitally important to cellular organisms.

The paper I presented showed that EPSP synthase shorter than 372 aa is functionally redundant; i.e. it is has no beneficial function whatsoever. The burden of proof lies on my opponent to provide evidence that an EPSP synthase shorter than 372 amino acids has any beneficial molecular function at all, as all observable evidence indicates it would have no function.


Proteins And Probability

Clark attempts to refute my argument from probability using two ways, (1) That probability is not entirely relevant as the EPSP synthase is not an end-product or an ultimate goal, and that (2) Natural selection can account for the origin of EPSP synthase and that therefore probability is not affected.

I will first articulate a response to no. 1.

All evidence is based on probability. Indeed, using Clark’s logic, the evidence for evolution would collapse—particularly those such as endogenous retroviruses or the arrangement of the geologic record.
For example, Darwinians claim that the probability of endogenous retroviruses inserting themselves randomly into a host’s genome yet displaying a beautiful evolutionary tree is next to nil.
However, using my opponent’s logic, the probability is not next to nil as there is no goal ‘in mind.’ All evidence is based on probability, whether or not there is a goal to be reached.

Next, my opponent says:
“The point of this, of course, is that if the steps on the way to making a final protein already exist in some forms and provide a selectable advantage, that any calculation which assumes that its evolution must start from scratch are invalid.”

The problem that in papers written by Durston, Abel, and Trevors there are no beneficial primary structures separating EPSP synthase from shorter functional proteins.
I’m not sure I fully comprehend the point my opponent is attempting to expatiate.

In Brief
In brief, intelligent design does not hold that there must exist some ‘god’ to better explain certain biochemical features, but rather merely an intelligent agent.
I believe all the evidence leads one to conclude that intelligent design is a better explanation for the origin and diversification of species.

Livingstone M.