I will begin my treatise by thanking my opponent Daniel “Theophage” Clark for his respect and civility and for his willingness to debate me. I want to thank him for taking his time in his response; his response has given me much food for thought.
Let me begin by clarifying one or two things; in the first place, the intelligent designer must not be supernatural. No one should argue against the proposition that some alien civilization constructed life and seeded earth with that life, or some similar paradigm. If this was true, the aliens could arise through unintelligent processes. But life on earth, it seems to me, is obviously intelligently designed.
In the second place, Daniel “Theophage” Clarke proposed that I hold that life was supernaturally created. This is not entirely true, and I regret I did not clarify this earlier. I do not believe in a model of special creation; the mechanism the intelligent designer used to design life on earth is not necessarily supernatural, it is guided. But indeed, it is true that I belong to the former class of intelligent design proponents.
Enclosed is my responses to Daniel “Theophage” Clark in the following format:
· A Reply To Clark’s “My Responses”
· The Genetic Code
· God of the Gaps?
· The Use of The Term ‘Darwinian’
· Amino Acids
· Protein Primary Structure
· Probability And Protein Primary Structure
· In Brief
A Reply To Clark’s “My Responses”
While it is true that I am asking for a plausible mechanism for the origin of DNA from RNA precursors, this is a rather trivial point. The difficulty in fact lies not in DNA arising from RNA precursors through unintelligent processes, but in the generation of replication, transcription, and translation processes, i.e. the various functions of the entire central dogma of molecular biology and the evolution of potential biofunctions.
The Genetic Code
As Daniel “Theophage” Clark predicated, all living things use DNA molecules as their genetic material. Viruses need only RNA, but in order to reproduce it is a requisite for a virus to have DNA which is used from a host as in the case of retroviruses and other types of viruses.
I think the pillar of my argument is not how DNA arose, but how the entire central dogma of molecular biology and potential biofunction could evolve through unintelligent processes.
I do not hold that evolution cannot produce an increase in either complexity or information. Complexity in itself is extremely easy to produce through unintelligent processes, and new genetic information is acquired daily through exon-intron gene linkage structure. Furthermore, even if it was true that new genetic information could not be produced through evolutionary mechanisms, we should have no problem with an amoeba evolving into a human over successive generations as the amoeba has more information than humans do.
The proposition that the first life used RNA as genetic material is not entirely accurate. As stated above, viruses need a host with DNA in order to reproduce.
“How far could such protolife evolve in the absence of a heritable linear digital symbol system that could mutate, instruct, regulate, optimize and maintain metabolic homeostasis?” –David L. Able, “The Capabilities of Chaos and Complexity.”
The evolution of potential biofunction in the genetic code cannot be explained by natural selection. Natural selection can only select what there is to be selected for. Selection pressure favors only existing biofunction.
God of the Gaps?
I do not think I am invoking a God of the gaps argument; if the probability of the evolution of life, for the sake of arugment, is 1 x 100^100 then I postulate that it is entirely accurate to propose that this is evidence of intelligent design. Intelligent design does not invoke supernatural entities; it merely states that intelligent intervention explains the origin of life in a far more adequate way than unintelligent causation.
The Use of the Term ‘Darwinian’
Stephen J. Gould, Elisabeth Vrba, and Niles Elderidge all identified themselves as Darwinians in contrast to saltationism and other proposed mechanisms of evolution. ‘Evolution’ simply means ‘unfolding.’ An evolutionist merely believes in the common descent model. A Darwinian believes in common descent through an accumulation of beneficial micromutations.
Amino Acids
I do not believe my text contained the answer to the problem of homochirality. The proposition advanced by Daniel “Theophage” Clarke, while ingenious, is prone to the underlying errors.
Virtually all chemical reactions produce racemic mixtures of amino acids, producing L and D aa in equal amounts. However, life has various regulatory mechanisms to ensure that only L types of amino acids are produced. Therefore, the very nature of chemical reactions would prove that the concept that natural selection played a role is somewhat flawed.
Origin of life hypotheses have failed miserably in their attempts to explain this phenomenon through biochemistry.
DNA and RNA strands are unable to bond complementary pairs without consisting of only one entantiomer. This means that DNA and RNA would be unable to reproduce in the protolife world without the issue of chirality being overcome.
Punctuated chirality, indeed, is an interesting hypothesis. However, this means that chirality would have had to be overcome before the evolution of a heritable prescribed symbol system, and this is where the fundamental error lies.
Protein Primary Structure
Daniel “Theophage” Clarke is indeed stating a truth in that this argument is an argument from improbability.
While many arguments from improbability are fallacies (like the creationist one on the probability of a million monkeys typing out a book applying to biology), I believe that in this particular case it is not an erroneous suppostion.
Daniel “Theophage” Clark then states that since I am asking how proteins became so complex, it is the same as asking how genetic mutations occur.
The mechanism proposed by Daniel “Theophage” Clarke is one of the mutating of codons that code for proteins.
However, this is not the bulk of my argument. It is not an argument from complexity, but rather an argument from functionality.
I regret that I must go into technical details here, but I cannot think of any other way to demonstrate my argument.
I mentioned the case of alpha/beta class proteins but I will use another protein here to demonstrate my point, i.e. EPSP Synthase.
A simple search of the Protein Information Resource (PIR) demonstrates that the primary structure of EPSP Synthase is composed of around 400 to 450 amino acids, depending on the organism. However, a paper by Durston K. Kirk [Kirk, “Measuring the Functional Sequence Complexity of Proteins.] shows that EPSP Synthase depends on 372 amino acid residues to maintain its function. In other words, the non redundant form of EPSP Synthase demands 372 amino acids.
Using this data, we can use the following table to measure the redundant protein sequences separating various proteins:
Near the number ‘400’ we can locate EPSP Synthase, and we notice that a functionally redundant space of 100 amino acids separates it from shorter protein structures.
This means that natural selection can play no role whatsoever, as there are virtually no beneficial sequences between EPSP Synthase and shorter proteins. Natural selection would have to sift through an endless array of redundant protein sequences before finally hitting upon the right sequence and that is the sequence of EPSP Synthase.
Using the above information, we can calculate the probability of EPSP Synthase evolving through blind chance alone:
The number of all possible sequences, i.e. the probability, is W. The length of each possible sequence is N. The number of possible options at each site is m.
Therefore, to calculate the probability W=m^N [Durston, “Measuring the Functional Sequence Complexity of Proteins.].
Thus, m would be 20, as this is the the number of possible options at each site in the sequence (20 amino acids), and N would be 100 (the number of redundant sequences separating EPSP Synthase from shorter proteins).
Thus the probability of EPSP Synthase evolving through randomness and chance alone, is 1/20^100.
This is a massive number, and I therefore feel that intelligent design is a far more adequate explanation for the origin of proteins.
While the first life would not requisite EPSP Synthase, protein evolution is a major obstacle for Darwinians. This is why I present the problem of protein evolution. It is not an obstacle to the origin of life in itself, but it is a barrier to the diversification of this life, i.e. the diversification of protein families.
Probability And Protein Primary Structure
I realize that my above treatise on protein primary structure may be a little too technical for some of the spectators. I will therefore demonstrate my position through an analogy, i.e. through a deck of cards in a poker game. Hopefully all of you are familiar with how the game of poker is played.
Let all of the various hands in the poker game represent protein functions. Three of kind for example, will present a short protein, and a royal flush an extremely long and complex protein.
Below are the hands used in poker, from lowest to highest in value:
One pair.
Two pairs.
3 of a kind.
Straight.
Flush.
Full House.
Four of a kind.
Straight Flush.
Royal Flush.
Therefore, one pair would represent the simplest protein function, and the royal flush would present one of the more complex proteins. Redundant sequences are represented by all of the possible combinations of cards that have no value in a poker game, such as a two, a four, a five, a seven, and a queen.
With this in mind, we can continue.
Therefore, the probability of getting a ‘one pair,’ is 1 in 2.3 (if you wish I can supply the math). 1 in 2.3 is quite a small number, and there is a high probability of getting such a number. The probability of getting a ‘two pair’ in a poker hand is 1 in 21.
Now, the probability of getting three of a kind is 1 in 47. This means, that, in terms of proteins, there are over 40 redundant sequences separating the function of ‘two pair’ from the function of ‘three of a kind.’
The probability of getting a straight is 1 in 255.
The probability of getting a flush is 1 in 509.
The probability of getting a full house is 1 in 694.
The probability of getting a four of a kind is 1 in 4165.
The probability of getting a straight flush is 1 in 64,974.
And the probability of getting a royal flush is 1 in 2,598,960.
One will invariably notice that the probability of getting the above hands decreases expotentially. I hold that the same applies to protein evolution.
In Brief
In conclusion to this treatise, I must say that my opponent wrote a well thought-out and reasoned reply. My opponent’s treatise was a very thorough, and I would like to thank Daniel “Theophage” Clarke for his excellent response.
So let the way wind up the hill or down,
O'er rough or smooth, the journey will be joy:
Still seeking what I sought when but a boy,
New friendship, high adventure, and a crown,
My heart will keep the courage of the quest,
And hope the road's last turn will be the best.
(Henry van Dyke)
Livingstone M.
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