An Analysis Of Clark's Critique

AN ANALYSIS OF CLARK’S CRITIQUE

In this essay, I will only analyze and respond to Daniel’s pivotal points and arguments – if there is anything which Daniel believes I have not responded to, please feel free to point them out and I promptly will correct that.

A Necessary Adaptation

I realize that I am tending to argue in terms of ‘best explanation,’ instead of in terms of ‘necessity.’ I also realize that it is my duty in this debate to demonstrate that intelligent design is necessary for life on earth. A necessary adaptation is therefore heralded – an adaptation which promises to demonstrate that intelligent design is necessary to account for life on earth.

That intelligent design is necessary to account for life on earth is to me a patent certainty – however the burden of proof is necessarily upon me to prove the above proposition articulated.

How then, can we prove that intelligent design is necessary to account for life on earth? What form of argumentation would demonstrate that intelligence is a sine qua non for life on earth?

Perhaps it would be best to introduce an analogy in this form: namely, that intelligence – rational design – must account for the origin of archeological features like Stonehenge.

The Darwinians should ponder long and hard on the question of how archeologists came to that inevitable conclusion that intelligence is necessary to account for Stonehenge.

It may interest the Darwinians to know that there is a not a scrap of paper of any civilization which claims to be the creator of the Stonehenge; true, there are tools around Stonehenge, but to argue that this is sufficient evidence to conclude that Stonehenge was designed by intelligence is as equally fallacious to argue that finding a Neanderthal hammer and other stone tools in a cave demonstrates conclusively the cave was built by the Neanderthals (I doubt anyone would argue such) instead of the cave being hollowed out by weathering processes.

The Darwinian is therefore met with this to consider: that intelligence is a necessity for the origin of Stonehenge.
Why is intelligent design an absolute necessity for the origin of Stonehenge?

We are met with an inevitable series of propositions which defines the process used to come to the conclusion that intelligent design is paramount and necessary to the origin of Stonehenge:
Firstly, that there is no known undirected process which can account for the origin of such a structure manifested by Stonehenge;
Secondly, that there is a directed process which can account for the origin of Stonehenge;
Thirdly, that this process can be experimentally verified and tested by replicating the construction of Stonehenge, and that this process which utilizes intelligence is an observable reality. That process is human intelligence.

The archeologist – and the Darwinian – now comes to the simple yet eloquent conclusion that intelligence is a necessary feature for the origin of Stonehenge. If Daniel disagrees with my above process to come to the conclusion that Stonehenge demands intelligence, I ask him to describe the process entailed.

What then, precisely, is the problem with using the same method to conclude that intelligence is necessary for the origin of life? I can find none whatsoever.

Therefore, my postulate that intelligent design is necessary to account for life on earth follows this curve:
[Assuming that all of these propositions are correct – I am using this method merely to demonstrate my point.]

Firstly, that there is no known undirected process which can account for the origin of protein primary structure;
Secondly, that there is a directed and intelligent process which can account for the origin of protein primary structures;
Thirdly that this process can be experimentally verified and tested by replicating the engineering of protein primary structures.

Therefore, we conclude – using the exact same process used to determine that Stonehenge demands intelligence – that intelligence is necessary to account for life on earth.

Mainstream Science vs. Clark

It is argued by those that hold that intelligent design is not necessary to account for life on earth – such as my opponent, Daniel – that intelligent design does not offer a more adequate explanation for certain biological features (such as protein primary structures) than Darwinian processes.

I believe that Daniel is articulating a false dichotomy between intelligent design and nature. Intelligent design is entirely natural – as equally natural as humanity or other species of organisms.

Furthermore, it may be surprising to learn that in this particular case mainstream science conflicts with Daniel – namely that scientific discipline of anthropology and the forensic sciences.

There is a process archeology uses to detect design in various objects. Naturally, lack of knowledge of how something was manifested does not amount to evidence of intelligent interaction. What does amount to evidence of intelligent interaction in archeology is the knowledge of how some phenomena could possibly have been produced through intelligent interaction (and how this phenomena is made through observable reality) while there is no knowledge of how this phenomena could have been produced without intelligence. This is the means archeologists detect design. This is the same means used by the forensic scientist and the detective. This is mainstream science.

This also happens to be the same method I am using to detect design: firstly, that there is the knowledge of how certain long protein primary structures could be designed and are designed through intelligence, and an utter lack of knowledge on how they could be produced through un-intelligent processes. Thus, I am entirely utilizing the methods used by archeology and the forensic sciences to detect intelligent design in biological features.

I therefore feel inclined to ask, “How is it that such methods of detecting design may be used in archeology and in the forensic sciences but that exact same method cannot be used to detect design in the biological world?”

I think the answer is very simple: there exists, whether one wishes to believe it or not, heresy in science.

Heresy In Science

At first glance, it may seem ludicrous at best to suggest that there is such a thing as heresy in science. But I am not alone in the opinion that there is such a thing – I am backed by the Encyclopaedia Britannica as well as evidence.

Is Daniel not aware that in 1906 Scientific American ran an article debunking the Wright brother’s airplane and posing them as frauds? Was this because it is indeed true that the Wright brothers did not invent the airplane, or that the airplane actually does not exist? Or is it because of willful intolerance of the unorthodox in scientific circles?

Is my opponent not aware that Nature, a peer-reviewed scientific journal, turned down Encrio Fermi’s work on beta decay because they claimed it was too remote from reality – and that they only published it after Fermi’s work had been widely accepted in scientific circles?

I do not think an ‘appeal ad mainstreamus scientia’ is sufficient to convince me that I am wrong in this debate – nor do I think it is an adequate argument against my articulations.

Answering Questions
Daniel posed a list of questions concerning mechanisms the designer could have used to design various biochemical structures and features. I will quote his point-by-point critique and then examine where it does not work:

Speaking of ribosomal engineering to account for the origin of the genetic code,
“Well, that is certainly a possible explanation, but again you have no evidence of an intelligent being utilizing those processes, nor any evidence that those processes in particular were used other than to say that it simply could have been that way.”

It would be interesting to hear a response to this from an anthropologist. Again, one must simply look to Stonehenge. Why does one conclude it is designed? Because of the process I described above. This is the same process intelligent design proponents use to detect design.

Expatiating on homochirality and chiral pool synthesis, Daniel says,
“Again, we have possible processes, but what is the evidence that these processes were used? Where is the archaeological remains of the facilities in which these were done, or of the intelligent beings which did them? None?”

I happen to live in that ultimate and universal structure which serves as shelter for the person of average intelligence, a house. However, I can assure you that around my house one will not find a single tool that would indicate it was constructed through intelligence.
Or better yet, to make an example,
If I constructed a small shelter made of just timber from the forest (sticks forming sides and walls) and then left it, and one year later archeologists found it, would they conclude it was intelligently designed or that it sprouted through chance processes? Naturally, the archeologists would suspect the latter – that this magnificent and beautiful little shack was the result of chance processes alone – that this singularly marvelous shack was the result of branches and twigs falling into place; and that it was also the result of rope flying in by the wind and through chance alone tying up the boughs and branches and twigs in the correct spots. This is what the anthropologists would undoubtedly conclude as there would be not a tool to be seen, or any ‘trace’ of intelligence whatsoever.
The more radical anthropologists, however, in a tone slightly different than that of their brethren, would say that chance is not a more adequate explanation for the origin of this shack, but rather that chance processes and intelligence are as equal in their explanatory powers.

Daniel says,
“why this instead of that, why is this virus using RNA and this one using DNA, etc.”
Since I still cannot grasp the point of this question, I will ask Daniel to list specifics. What virus? What anatomical part of what creature? Etc.

On Probability

In his latest exposition Daniel wrote the following:
“The simple fact is that functioning life reproduces and makes more functioning life, and non-functioning life (if it can be non-functioning and still live) does not. That is simply an observation about what obtains, not any kind of evidence of a goal.”

Naturally, the individual molecules, taken as a single entity, are not goal-oriented. The same holds true for the card analogy. However, there is a goal in life. That goal is survival. Life is a constant struggle to survive – a never ceasing struggle to be the fastest runner, the highest flier, the strongest creature, the best swimmer – all of these things are invariably dictated by the functionality of protein primary, secondary, and tertiary structure. It is therefore quite patent that there is a goal even in protein primary structures.

Daniel also says:
“Livingstone, please show us how you calculate the probability of life functioning that isn't just a re-hash of the bad probability argument that you gave at the beginning.”

I see no problem at all with using the formula W=m^N to calculate the probability of said case – where W is the probability factor, m is the number of possible options at each site, and N is the number of possible sequences.

Daniel further request that I show my figure that functionality is rare. My argument is not that functionality is rare; however, protein primary structures separating exceedingly long, functional protein primary structures, there is a general lack of functionality. In this particular case, functionality is rare.

Finally, Daniel says,
“Remember, functionality is not just a matter of the individual protein or other molecule itself, but the system the protein finds itself in: Protein A may be perfectly functional in environment X, but fail to do anything in environment Y. How you're going to work that into your calculations should be interesting.”

Firstly, let us all remember this: that proteins find themselves in cells. Secondly, that codons are what code for amino acids, and amino acids are what constitute protein primary structures.
I accept the definition of functionality as proposed by the paper I cited in an earlier post regarding protein functionality – i.e., it can mean specific biochemical reactions, cellular responses, or molecular components that interact with biocatalysts.
Thus, a functionally redundant protein primary structure would be devoid of all of those manifestations, and more than that as well. It can be regarded as an inert polymer in such a case. Consequently, I could care less about the environment the protein is in. Whether the cell finds itself in a boiling hot-spring or a freezing wasteland of the North, it is completely irrelevant.

Semantics
Daniel asked a question concerning my continual use of the word ‘protein primary structure’ and asked me why I did not instead use the word ‘gene.’ The answer is very simple:
I use the word ‘protein primary structure’ to clearly distinguish between protein secondary structure and protein tertiary structure.




All About Nylonase

I still postulate that nylonase evolved with no intelligent direction because virtually any mutation that occurred at the chromosomal loci that codes for the enzmye of which it is a derivatice would be functional – and not only functional but a step towards the evolution of nylonase.
However, in the case of EPSP synthase, PB2, S12, or any other proteins that have been sequenced and their functionality determined in vitro, there is a barrier which I believe I proposed before which would impede the evolution of such proteins.
The burden of proof is on Daniel to demonstrate that the case of nylonase is parallel to the case of the above proteins I mentioned – in that there is a barrier of functionally redundant protein primary structures separating one protein from another.
I have furthermore evidence to support my hypothesis that nylonase was not subject to any such barrier:
“Scientists have also been able to induce another species of bacteria, Pseudomonas aeruginosa, to evolve the capability to break down the same nylon byproducts in a laboratory by forcing them to live in an environment with no other source of nutrients. The P. aeruginosa strain did not seem to use the same enzymes that had been utilized by the original Flavobacterium strain.”

This means of course that a different set of codons were utilized by one bacteria than another bacterian, but the end result was the same: nylon was digested. This means that my hypothesis has some substantiated evidence to back it up.

However, Daniel makes this statement:
"Livingstone cannot claim that there is no possible way for it[EPSP synthase] to evolve when there is, and that is exactly what he needs to claim in order to show that the intelligent design of this protein is necessary as per our agreed upon debate topic. That is my point."

There is a monstrous difference between ‘possible’ and ‘plausible.’ It is possible that flying spaghetti monsters (no pun intended) exist, but we must ask ourselves, “is it plausible?”
Having said that, I think I have demonstrated that there is no plausible way for certain protein primary structures to evolve. I have done this through peer-reviewed articles I have presented in this debate. Indeed, if there were no such barriers to protein evolution then that would be the death of directed enzyme evolution. Directed enzyme evolution is needed to engineer certain enzymes for specific functions simply because there is a barrier that Darwinian mechanisms cannot pass.

Responding To Critiques

On nylonase, it is not necessary for the enzyme to be arrived at one single step – it may take many steps for nylonase to evolve. However, nearly all of these steps entailed would be functional and beneficial to the bacterium. This would allow natural selection to select the gradual evolution of the nylonase.
I quote Daniel,
“It is almost assured that many mutations were tried and the right one came up and was therefore used; that's the way evolution works.”

It is almost assured that Daniel did not venture to cite a source that indicated that ‘many mutations were tried and the right one came up.’ Indeed, it is almost assured that many mutations occurred and those bacterium that were more capable of digesting even a little nylonase survived better. It is almost assured that there was no one singular mutation that was ‘right.’ Rather, a series of progressive mutations occurred, slowly leading towards the evolution of nylonase.
I am not saying this based on mere assumptions; my postulate that in the case of nylonase every protein primary structure that formed was functional and therefore capable of being selected still stands and with evidence (which I wrote above on the case of different strains of bacteria being used).

In the case of citrate, who is to say that it is not the same case of nylonase, where there is not an impassable and monumental ‘protein barrier’ separating the enzymes which evolved the ability to synthesize citrate?

I quote Daniel again:
“The fact that some sequences of numbers (analogous to genes and the proteins they make) may not "work" when combined with their environments (including other numbers they reside with) may make the journey from one to the other more difficult and indirect, but you've got to have a lot more evidence that you absolutely can't get there than what my opponent has presented, or indeed, opponents of evolution have been presenting for the last 150 years.”

More difficult and indirect is quite clear – indeed it renders it most unnecessary to construct any form of elucidation. By more difficult and indirect my opponent undoubtedly means that trillions upon trillions of mutations would be needed. By more difficult and indirect my opponent necessarily is meaning to say that great gulfs consisting of trillions of functionally redundant primary structures can be – even though it is ‘more difficult’ – through an indirect method inevitably crossed. I suspect this is what Daniel is implying. If not, I ask him what he does mean.

Necessarily, the Darwinian will acknowledge that chance processes alone are sufficient to account for exceedingly long protein primary structures which have function. Even though chance processes have never been observed to account for such protein primary structures the faith of the Darwinian in pure-chance processes remains unshaken.

Daniel asks a very interesting question regarding the hypothetical ET engineers. His question can be summed up thusly: why would these aliens who, having no genetic code, design life on earth with an inheritable system other than the prion system, i.e. with a genetic code?
At first glance, this question sounds quite reasonable. However, there is an answer to the above question, and an answer which required little reflection on my part. Prions cannot, to my knowledge, be subject to genetic engineering. It cannot be subject to recombinant DNA techniques and cloning. Prions cannot be designed through directed enzyme evolution techniques coupled with recombinant DNA. Therefore, these hypothetical alien engineers would have to design a genetic code that would ensure that they could engineer many different types of organisms. This is quite patent and clear.

Lastly, I will respond to Daniel’s critique of the intelligent designer finishing the design some 200,000 years ago (actually a little more than that).
Daniel writes that,
“I cannot help but again think that it is just a biased and anthropocentric view that intelligent design ended with mankind.”

Yes I suppose it is extraordinarily biases and particularly anthropocentric. Indeed, its anthropocentricity is, in all probability, nearly equal – or even as equal as Charles Darwin’s extremely anthropocentric statement in The Descent of Man Chapter 6,
“The Simiadae then branched off into two great stems, the New World and Old World
monkeys; and from the latter, at a remote period, Man, the wonder
and glory of the Universe, proceeded.”

I expect a flow of rhetoric on Charles Darwin’s bias, his notorious anthropocentricity – it should be condemned by all of those who hold that man is not the wonder and glory of the universe – not the most-highly developed species of organisms on earth.
I still hold that it logically follows that, as the development of the species follows a general curve from crudely formed to a more highly developed state, intelligent design concluded with man. This is in itself is evidence of when the intelligent designer stopped its design, i.e. human designers designed things following a curve of less developed to more developed. I see no practical refutation of my point here.

In Brief
I think that I have in fact come up with a considerably large body of evidence and substantial arguments to support my thesis, despite what Daniel says that ‘lack of evidence seems to be a recurring theme here…’

I am supporting my thesis with the same processes used by mainstream scientific disciplines like anthropology and forensics, and even SETI science.

I am quite sure that the facts and evidences already advanced render it undeniable that intelligent design is a requisite and a necessity to account for the origin of life on earth.

-Livingstone M.