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.

Theophage's Second Response (or Round 2: Evolution Boogaloo)

They say imitation is the sincerest form of flattery, and I do appreciate the effort on my opponent's part to format his response a little closer to the way I did mine. But that isn't really necessary, I saw nothing wrong with the way he formatted his opening statement and I think things are going well. It seemed like he was trying a bit too hard. He especially doesn't need to use my entire name (including nickname/handle) every time he refers to me either. Daniel, Mr. Clark, or just Theo is perfectly fine, I think our audience can figure out who he is referring to. Repeating the entire thing sounds somewhat forced and stilted.

But repeatedly adding the 'e' onto my last name? I'm afraid that sin is almost unforgivable. You'll have to do a lot to get back into my good graces after that, Mr. Livingstone M. ;^)

ET and The Grand Old Designer

Often in the literature and speeches of intelligent design proponents we hear that design is not necessarily referring to supernatural powers or beings; "it doesn't have to be God, it could be aliens" or whatever. My opponent, naturally, echoes this sentiment.

But are we really talking about aliens here? While technically correct, I suppose, I find such declarations to be disingenuous; a vestigial remnant of the attempt to get intelligent design taught in public classrooms by assuring us that it isn't about God and religion at all.

A very graphic example of this was brought to light at the 2005 Dover trial, where we learned that the intelligent design version of the creationist biology text "Of Pandas and People" was basically the earlier creationist version, just with the terms 'creation' and 'creationists' hastily cut and pasted over with 'design' and in one humorous case 'cdesign proponentsists"

It is also true that there is one "religious" group known as the Raelians that does indeed believe that life on Earth was designed by aliens. And those aliens by earlier aliens, ad infinitum. But do we really want to pretend that we aren't talking about God in this debate? Really?

Tools of the Designer

I say this not just to be provocative, but because I think it actually has some bearing on the detection of, and therefore the evidence for, design.

We already have methods to detect design in certain instances, such as identifying stone tools used by early humans. I have seen some examples that to my untrained eye look just like natural stones, but to trained anthropologists they are obviously intelligently created tools. Now I can tell an arrowhead is obviously an arrowhead, but some things just look like weird lumps.

One of the techniques used in the identification of these things is noting the results of how they were formed. The particular types of knapping, flaking, etc. used by the creators of these tools leaves behind evidence not only that they were made by an intelligent being, but also evidence of the process of how they were made.

Another example would the be the mysterious crystal skulls that have been featured everywhere from blockbuster movies to various Time/Life book series on mystical artifacts. It was by close examination that the details of how the skulls were manufactured were discovered, showing that they were not pre-columbian New World artifacts like most often claimed, but produced in various places in 19th century Europe. The skulls were considered intelligently designed in both cases, of course, but the point is that by studying the evidence left by methods used in their making, the actual identity of the designers is more readily...uh...identifiable.

It would seem, then, that the prime method for detecting design in life should be the detection of the methods of the hypothetical designer, either by natural but alien technology or ineffable, supernatural magic. Surprisingly, we find that the history of the intelligent design movement is a history of doing the exact opposite.

From Paley with his watch analogy, to Behe with irreducible complexity to Dembski and his complex specified information, proponents of design have invariably sought evidence for design in life by life's intrinsic properties alone, not by trying to identify the methods by which the hypothetical designer of life would have or could have done his work. This is the very reason why I believe that all of these attempts have failed so far.

Mysterious Lab Visitors

So let's look at a concrete example. Quoting from Wikipedia:

In 1975 a team of Japanese scientists discovered a strain of Flavobacterium living in ponds containing waste water from a factory producing nylon that was capable of digesting certain byproducts of nylon 6 manufacture, such as the linear dimer of 6-aminohexanoate, even though those substances are not known to have existed before the invention of nylon in 1935. Further study revealed that the three enzymes the bacteria were using to digest the byproducts were significantly different from any other enzymes produced by other Flavobacterium strains (or any other bacteria for that matter), and not effective on any material other than the manmade nylon byproducts.
from http://en.wikipedia.org/wiki/Nylon-eating_bacteria

So we have a bacteria using certain newly bestowed enzymes to perform a function which it's predecessors did not have. For those of us firmly in the evolutionary camp, this is not surprising given the power of mutation and selection. For most of those in the intelligent design camp, it is also easily explainable as the action of the Grand Old Designer giving the bacteria the new ability. Apparently, the designer once again did that voodoo that He does fairly recently.

Later in the wikipedia article, we also read this:

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. Other scientists were able to get the ability to generate the enzymes to transfer from the Flavobacterium strain to a strain of E. coli bacteria via a plasmid transfer.

Again for those who accept modern evolutionary biology, there is nothing surprising here, just mutation and selection. For the intelligent design advocates, however, it would seem that the designer really wants those particular populations of bacteria to be able to eat nylon and nylon byproducts for whatever reason.

Now for those who believe the designer is an omnipotent, omniscient, and omnipresent God, then His ability to tweak life wherever and whenever He wants is quite understandable. But for those who hold that it is aliens doing the interfering and designing, is it really equally probable? Were the aliens spying on the lab and waiting for the scientists there to conduct their experiments just so they could break in during the night and intelligently engineer the results? Should all biology labs now be on high alert due to possible interference from aliens in their experiments?

I do not know my opponent's position on this particular discovery, nor whether the bacteria's new ability consititutes true intelligent design in his mind, but I think this example serves to show that there is a huge difference between intelligent design by hypothetical aliens and intelligent design by a hypothetical God at the very least by the criteria of opportunity. Methodology would certainly be more telling, of course, if any could be found.

I would appreciate it if we could simply both admit that the hypothetical designer we are debating about here is God, not aliens. I think that would be more honest. I think I would place the probability of such aliens existing and at work here at least as low as my opponent places on purely natural processes at work. I also apologize for taking such a long detour to make such a tangenital (though I think important) point.

The Known and The Unknown

Though Livingstone is apparently much more familiar with the various biological specifics than I am, all of the arguments he has put forward so far seem to boil down to only two main themes: 1) modern biology cannot explain how (by what specific processes) X could have happened, and 2) the probability of X happening by chance is so low that we can effectively discount it. The unspoken assumption here is that if neither known physical processes nor mere chance alone can account for what we see, then intelligent design, by whatever possible designer utilizing whatever possible methods, is the most reasonable explanation. This is exactly the line of reasoning used by William Dembski in his explanatory filter heuristic.

But the same problems which plague Dembski's arguments are the same problems which plague my opponent's: how can one tell actual design from simply an unknown but unintelligent natural process? Unless you have some sort of method of differentiation, then no real determination can be made except by parsimony, and parsimony (also known as Occam's Razor) necessarily eliminates the design option. Let me give my justification for this:

For both the proponents of unintelligent evolution and intelligent design, an unknown process must be postulated. But in addition to an unknown process, design advocates also require the existence of an unknown designer as well to put their unknown process into effect. Since parsimony tells us we should not multiply entities needlessly, unless there exists some additional evidence for an intelligent designer (or at the very least, a dicovery of the designer's methods) then the most reasonable explanation to such mysteries is an unknown unintelligent process.

This is what Dembski recognized as he tried to tie intelligent interaction exclusively with what he called 'complex specified information' or CSI. Clearly, if there was a type of organization which could only come from an intelligent source, then that would be exactly the type of evidence needed to distinguish an intelligently guided process of unknown methods from an untintelligent unknown process. But Dembski failed in this attempt, as Wesley Elsberry has shown that unintelligent and Darwinian evolutionary computer algorithms can produce exactly the kind of CSI he was asking for.

Now my opponent has not brought up CSI or Dembski so far in this debate, he seems to be satisfied with merely showing that there are either processes that are not currently explained or products which are practically impossible by chance (as per the explanatory filter), and calling that evidence for intelligent design. This is simply not good enough for the reasons outlined above.

He must give either a) evidence of the designer, b) evidence of the designer's methods, or c) show that physical processes needed to account for these things are not merely unknown but impossible in order to affirm his case that intelligent design in necessary for life. Can he do this? I don't think so, but I am very interested in watching him try.

And now some specific points:

The Use of the Term ‘Darwinian’

I certainly concede that the term Darwinian has an appropriate usage to distinguish from markedly non-Darwinian ideas, and I apologize if I jumped the gun and made a bigger deal than warranted over minutia. But I still don't feel that the word is very helpful or informative or accurate in the context my opponent used it. He wrote:

"The existence of a genetic code is perhaps one of the most devastating arguments against Darwinians who believe life can arise through unintelligent processes."

While it is apparent that Livingstone meant the term to distinguish those who hold that evolution consists solely of unintelligent naturalistic processes from those that don't, the problem is that the people like me who hold that proposition also accept many decidedly non-Darwinian yet still unintelligent and naturalistic processes such as genetic drift, endosymbiosis, and horizontal gene transfer. So it just feels odd to call such people "Darwinians" in this context.

But again it is only a minor thing, so I won't digress this way any further. (I go on and on way too much as it is :^)

Amino Acids

This is an example of an argument that my opponent uses of the form: "modern biology cannot explain how (by what specific processes) X could have happened" and therefore intentional design better explains it. But as I wrote earlier, intentional design has to suppose both an unknown designer and an unknown process by which the designer implements the design in order to explain the phenomena, while mainstream science simply has to suppose an unknown process. Parsimony is our only guide without some specific evidence to determine which explanation is correct.

Is there specific evidence of intelligence at work? Is there specific evidence that unintelligent processes not only do not but cannot be responsible? That is what my opponent needs to provide, not merely pointing out what science currently does not know. (I'm sure that list would be near infinite!)

In his last post, he writes:

"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."

Note that it is not all chemical reactions that produce equal amounts of both L and D types, only most of them; certainly including the most common types of reactions. So yes, some more complex or uncommon chemical reactions do produce only one type. If it were impossible to do so, if there were no possible chemical reactions which could do this, then perhaps my opponent would have a point.

He also writes:

"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."

So let's try to envision this problem in an RNA world. The simplest replicators could hardly even be called 'alive', and it is quite possible that they didn't even have some of the qualifications for life (metabolism for example), but what they did do was replicate. As I'd mentioned in my previous post, there are particular known RNA sequences which are fully capable of replication all by themselves; they don't need other molecules to act as helpers like DNA does. A Science Daily article about this can be found here: http://www.sciencedaily.com/releases/2009/01/090109173205.htm

If what Livingstone says above is true, and complimentary pairs could not bond without being the correct handedness, then it seems to me that such simple RNA could only successfully reproduce once it has bonded all of its complimentary pairs. Which means it would simply 'swim' through the mixture, bonding when it encountered the correct individual amino acids, and when it was done, it would split and now have two copies of itself to continue the process.

So again, it would seem (and this is only to my limited undertstanding of the process) that the fact that the wrong entantiomer makes the process not work would provide a selection pressure. Once you have replication and variation, regardless of actually having 'life', you will still have Darwinian natural selection at work. Living things, then, are simply refinements and improvements of that original process.

The Genetic Code

Again we have what seems to be an argument of the form: "modern biology cannot explain how (by what specific processes) X could have happened and therefore intentional design better explains it." Although my opponent wrote:

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 don't actually see a difference between the two, they seem to me to be inextricably linked. If you think it is important and makes a difference to your case, Livingstone, please explain the difference you are making here.

But regarding a RNA precursor to DNA, my opponent wrote:

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.

While this statement is true, I think it misses the point I was making. Not all viruses use RNA as heritable material. Some use single strand DNA and some use good old double strand DNA just like us metazoans. And yet even these viruses require other living cells to reproduce.

This is not an inherent defect in what molecule they are using for genetic material, it is simply the way these viruses are structured; they have evolved to need other living things and have specialized to the point where they don't carry all the molecular machinery needed for their reproduction. If I had tried to make the case that these viruses were examples of the proto-life on the early Earth, then this objection would have been valid. Instead, however, I was merely pointing out that some things still use RNA for heritable material, even if those things have other reproductive difficulties.

Finally in this section, Livingstone wrote:

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.

I certainly agree with most of the above, particularly that natural selection does not and cannot select for "potential biofunction". But when we are talking about the origin of life, we aren't talking about merely Darwinian processes. These only apply once you already have some sort of replication process, and some variation in that replication.

Where it seems my opponent is going wrong is in the apparent assumption that the earliest replicators used their genetic material in the same way that present organisms do. We use our genes to code for body plans which are realized through development by the complex machinery of the cell.

But the earliest life would not have had these processes, nor much of a 'body' to develop, nor would have they needed them. As I mentioned above, certain completely naked RNA molecules have been found to self-reproduce. Once we have reproduction and variation (variation, of course, comes from imperfect reproduction), then we do have something for natural selection to act upon. More successful replicators and more successful replicating systems would dominate, and everything else is simply an addition and an improvement upon this.

It is not as if life said to itself, "You know, I'm going to need a complex system of being able to code for proteins to generate a body, so I'm going to need molecules that do this and this and this..." It is much more likely that the first replicating molecules and molecular systems were simply converted over to those functions as the need arose and the complexity added by mutation allowed. To assume otherwise is to put the cart well before the horse. The system we use today is not the intended end-product, but simply a finely adapted variation of original function.

For some possible examples of early life and abiogenesis processes, I recommend some videos by YouTuber cdk007:
http://www.youtube.com/user/cdk007#grid/user/0696457CAFD6D7C9

Protein Structure and Function

In this section, my opponent is using both the "cannot explain how" argument and the "probability of X happening by chance is so low that we can effectively discount it" arguments. Let's deal with the first one first.

When speaking of particular proteins and particular functions, there seems to be an assumption made that only a particular protein will work or that only a particular function is necessary. This is the essence of the irreducible complexity argument as proposed by Michael Behe, though reduced to a single protein or function rather than a system.

But as refutations of Behe's arguments have shown, IC systems can still evolve naturally due to several already known biological processes such as scaffolding and co-option. Since the particular problem given by my opponent (the EPSP synthase) seems to be of this nature, I contend that the solution to said problem probably falls within these possibilities.

For example, let's go back to the nylon-eating bacteria. It produces enzymes which break down the nylon products into food it can use. It's ancestors could not do this, and it cannot live on the food it's ancestors once did. How could this possibly evolve?

In the original paper on the organisms, it was proposed that what happened was a gene duplication and subsequent frame shift mutation on the copied gene. This created the new gene which coded for the enzyme necessary to exploit the new food source.

In a later paper this was found to be incorrect, but the wikipedia article gives plenty of links to other cases of this nature where gene duplication and subsequent mutation give rise to additional functions. And since this was the example I planned to use before I'd read that (I was surprised to read that the original findings were incorrect, and I am still unsure exactly in what way there were incorrect) I'm going to go ahead and use this example anyway; it is only a demonstration of the general idea.

In the case of the nylon-eating bacteria, it is not that the enzyme involved was designed to allow them to live in the extreme environment, it was that an accident allowed them to utilize a food source no one else had, and they subsequently specialized so that the nylon products were not just an optional, but a necessary food source. The enzyme went from beneficial bonus to absolute necessity.

You will note that in this example, it is not a case of the nylon-digesting enzyme evolving from a simpler enzyme with a similar function. This may be analogous to the EPSP synthase used in Livingstone's example. While it may be the case that there is no simpler predecessors with similar function it could have directly evolved from, that in no way bars it from having a history similar to the nylon-digesting enzyme in this example which seemingly popped out of nowhere and then became vitally necessary.

It may be that the EPSP synthase did not have the function that it's simplest form had, but in a simpler form had a different function that was co-opted for use in the present manner when the coding gene mutated and then later organisms specialized to the point which made that new function necessary. I do not know, as I simply don't have enough information about this particular case to say definitively (if indeed anyone has enough information to say definitively).

But for my opponent to claim that it cannot arise due to mutation and natural selection in some manner similar to this, the onus is on him to show that these possibilities cannot be the case. I do not believe he has done this with the information he has given us; his information only shows that a smaller than 372 amino acid version would not have had the same functionality. But this is clearly not the same thing.

Protein Structure and Probability

The other argument my opponent uses is one of probability. As I'd granted earlier, if it could be shown that the probability of a particular process was sufficiently low, then I would agree that we can consider it impossible to have taken place. My problem with the arguments he has given, however, are that the probabilities he gives and the assumptions by which he calculates those are simply incorrect.

In the example he gave, he calculated that the probability of the EPSP synthase evolving through random processes is around 20^100 to 1 against. Again, I would grant that such long odds mean that process would indeed be functionally impossible. But there are two important assumptions he is using in the calculation of that number: 1) that the EPSP synthase is the end-product intended, and 2) that the method of adding the 100 necessary amino acids was a one at a time random addition with no intervening selective pressures. Are these assumptions warranted? Absolutely not.

In regards to the first assumption, since my opponent used a playing card analogy I will as well. There is an important distinction between the probability of a particular needed outcome, and the probability of any possible outcome. If I take a deck of standard playing cards including the jokers and then deal them out into a 54 card sequence, the probability of that exact sequence appearing on the table is about 2*10^70, not quite the number that Livingstone gave us, but still a ridiculously huge number.

So what happened? Did a miracle just occur on the table? What if I shuffle and repeat this procedure again and again? The probability of each of the results that comes up is the same number, and yet they keep coming up. How can this be?

The difference is that the probability I calculated is if we are beforehand looking for only one particular sequnce of the 54 cards to come up. But that clearly isn't what we are doing when we are just dealing them out in whatever order they were shuffled into. Neither is that what evolution was doing when it came up with the EPSP synthase. It was simply going through the processes of mutation and natural selection; it had no goal protein in mind, so regardless of what the astronomical probabilities are of that protein being needed and formed by chance, that has absolutely nothing to do with how unlikely it is for it to have evolved.

This is the same poor assumption that all intelligent design proponents make when they offer these specious probability arguments regardless of what particular protein or molecule they want to discuss. But the argument doesn't work because the assumption that the end-product is what is being sought by random chance is simply false. Just as false as the miracle happening every time I deal out a deck of cards.

Even though that point alone is enough to refute Livingstone's argument from probability, there is also the matter of the second assumption that he makes. As I alluded to in the nylon-eating bacteria example earlier, each step in the evolution of a protein that performs some function need not have the same function as the end-product, in order to be influenced positively by selection.

As Kenneth Miller explains in his refutation of the problem of irreducible complexity in the evolution of the bacterial flagellum, one of the crucial flagellum pieces is simply one that has been co-opted from its original function as a type III secretory system protein. More information on this can be found here:http://www.millerandlevine.com/km/evol/design2/article.html

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.

Adding it all up

I'd just like to point out that I am not particularly hostile to the idea of intelligent design found in either life or the universe. It certainly could be the case, and a God could certainly exist somewhere and somehow. I simply haven't found good evidence that these things are true, and I have found what I consider good evidence that these claims are probably false. What is important is the quality of the evidence and argument provided to support these ideas.

My opponent in this debate is trying to support the claim that intelligent design is necessary for life to exist. I believe he cannot do this, simply because I believe this is not the case and thus the evidence cannot be there. But I am completely open to the idea that I am wrong, as is my opponent. I do not envy him this task he has set for himself, however.

Only a small part of what we debate these things for is to convince the other person that we are right. If past history is a guide, very few of the participants in these kinds of things end up being immediately convinced by the other side. But what I think is a more important purpose for these sorts of debates is the unique opportunity they give us to examine our own arguments, evidences, and assumptions in the harsh light of criticism. It may only serve to strengthen our own beliefs, but I think that strengthening is a desireable outcome regardless.

I have tried to point out, Livingstone, where I believe the assumptions you base your arguments on are false. I may or may not be correct in this, but I am sure that we will both learn some things before this debate is over. I know I have already.

Daniel "Theophage" Clark

At the speed of geology...

As if I didn't take long enough to hold up my end of the debate, I am currently in the middle of traveling. We have moved from our beloved home in Tucson, AZ to the frigid and inhospitable wastes of Battle Creek, MI to live with my sister. As I'm typing this, we are at the Days Inn in Tucumcari, NM.

Long and short of it, I probably won't have my regular post up until Friday or Saturday. My apologies to all who have waited way too long.

Daniel "Theophage" Clark

Livingstone's Response To Daniel "Theophage" Clark's Treatise

Introduction
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.

Theophage's Opening Statement: Intelligent design is *not* necessary to account for life on Earth

"You take the good you take the bad, you take them both and there you have ... my opening statement"
- Peter Griffin

An Introduction

First of all I would like to thank the YouTuber known as Theforthcoming1 for suggesting the idea of a debate between Livingstone and myself, and of course thanks goes out to Livingstone, or FirstFreedomFighter on YouTube, for graciously agreeing to a debate and suggesting the topic of evolution. I enjoy debates like these, and while I may or may not be getting into something way over my head, I will try to make it as enjoyable as possible while hopefully everyone involved, debaters and spectators alike, will have learned some things before we are through.

My job in this debate is to show that the statement "Intelligent design is necessary to account for the existence of life on Earth" is false. I do this because I believe that the natural mechanisms of physics and chemistry as well as the biological mechanisms of evolution alone are sufficient to account for life on Earth both in it's origin and in its current diversity.

There are actually two different ways in which an intelligent agent such as the Christian God may be necessary to account for life on Earth: either directly though the actual design and supernatural construction of living things, or more indirectly by the creation of the universe and the implementation of the right combination of laws and physical conditions to allow life to arise naturally.

The believers who hold to the former are generally known as creationists or intelligent design advocates and do not accept (or at least not wholly accept) modern evolutionary biology, and often other disciplines as well (cosmology, geology, etc.) Believers in the latter group generally have no problem with the findings of these scientific disciplines.

My opponent advocates the direct form of intelligent intervention rather than merely the indirect form. It is because of this (and because the indirect form is compatible with mainstream scientific findings that I also am in agreement with) that I will be focusing my efforts toward showing the the direct form of design is not necessary for life rather than arguing against the indirect form. If my opponent wishes to jump to the indirect form later (most probably by invoking the 'Fine Tuning' argument) I will be happy to do so, but only at that time.

So let's dive right in.

My Responses

I have to say that I was rather surprised when I read Livingstone's opening post. I expected something more along the lines of an introduction to his position as I gave above, but he jumps right in with both feet and gets much more technical than I expected. Looks like I'm going to have to do my homework.

It is interesting that while we were coming up with the specific topic and discussing the terms for this debate, I had specifically written the following to Livingstone:

"I think "I don't know" is a valid (though uninteresting) answer, certainly the most honest answer there is to a great many things. If we do a question back and forth thing and you hit me with: "So what was the first self replicating RNA, and how did that precursor eventually change into DNA? Answer that you exceptionally suave man of atheistic science!" my only answer to that question could be "I don't know" because I simply don't."

So what do we find among the first five points he wants to discuss? You guessed it: The origin of DNA from RNA precursors. Its like I'm Ralph Macchio and my opponent from Cobra Kai has just been told "Sweep the leg!" I guess I will just have to hope that my crane technique will be enough.

The Genetic Code

All living things today use DNA molecules as their genetic material except some viruses which use RNA instead, though it is often a point of contention whether or not viruses can truly be considered 'alive'. DNA is a very complex molecule and cannot perform reproductive and transcription operations on its own; it requires quite a few additional enzymes and RNA molecules to accomplish these functions. Given the complexity of this arrangement, it is not probable that the first living things used such a system. On this point, I think my opponent and I agree. What is more probable is that early life used a simpler system which evolved over time into the more complex system we see today.

Now some in the audience may wish to stop me right there. "Natural processes cannot produce an increase in complexity/information. That's why evolution is nothing but a lie!" I don't know what my opponent's exact position on this is, but I will be happy to provide examples that yes, evolution can and does produce increases in both complexity and information upon his request.

So what could have this simpler genetic material have consisted of if not modern DNA? Well, those pesky viruses give us a clue: some most definitely use RNA as genetic material. The idea that all living things once used RNA solely as genetic material which over time was replaced by the more successful but complex DNA is known as the 'RNA World Hypothesis' and more information on that can be found here: http://en.wikipedia.org/wiki/RNA_world_hypothesis

The reasons why RNA is a good candidate for a precursor to DNA is because, as I'd said, it currently is being used as genetic material by at least some things so it certainly has that capacity, and because it does not necessarily need all of the additional molecular machinery that DNA requires. Some RNA molecules are completely auto-catalytic and self reproductive, requiring nothing but the commonplace raw material in its environment to build more copies of itself with. This is exactly what we would expect to find if DNA truly did come from a simpler precursor rather than being created specifically as the only possible molecule of life.

This brings us to a very important point which will be echoed both throughout this post as well as probably throughout this entire debate: While it is certainly true that science does not have all the answers to all the possible questions about life and how it arose, and sometimes not even any hard specifics, it does not need to in order show to a reasonable degree that the intervention of a deity is not required as an explanation.

God of the Gaps

To argue that simply because we don't have some specific explanation for a particular phenomena, therefore God must be the explanation, is a fallacious argument known as invoking the 'God of the Gaps'. It is fallacious because there is a huge step between saying that some phenomena currently does not have a naturalistic explanation, and saying that the phenomena simply cannot have a naturalistic explanation, and those who use the argument wish to leap from the one to the other without giving any particular justification for such a huge leap.

I ask that if my opponent is going to use argumentation of this nature, that he give proper justification for why a naturalistic explanation for some phenomena or another isn't just simply unknown, but actually cannot exist. I can think of several possible examples of how he could do this.

For one, if it could be shown that no other molecule or system of molecules has the capacity for self replication and heredity except DNA and it's required compliment of enablers, then that would indeed be strong evidence that DNA could not have arose by natural means, since it could not have had any simpler precursors. Of course, we see already that this isn't the case.

Similarly, if the chemicals of life itself were not constructed of the same sorts of things (carbon, oxygen, etc) that non-living things are made of, and there was no way one could convert from one to the other, then that also would be strong evidence that living things could not have possibly arose from non-living matter. This in fact was widely believed until 1828 when the German chemist Friedrich Wöhler was able to synthesize the organic compound urea from inorganic chemicals, showing that there is not a definite distinction between the compounds used by life and non-life.

I'm sure, and I sincerely hope, that my opponent can think of other (and more successful) ways of showing that not only are there not currently naturalistic explanations for certain necessary requirements of life, but that there cannot be, and thus an intelligent designer of life is indeed necessary.

Darwinian

I just thought I'd point out something I thought kind of humorous (yeah, I'm silly like that) that my opponent said in his section on the genetic code:

"The existence of a genetic code is perhaps one of the most devastating arguments against Darwinians who believe life can arise through unintelligent processes.

The irony here, of course, is that Darwin himself knew nothing of DNA, RNA, or genetic codes, only that there was some nebulous but inherent mechanism for heredity. It would seem that a true "Darwinian" (presumably a follower of Darwin, though probably used as some sort of perjorative like "evolutionist") wouldn't even need to concern themselves with such advanced, futuristic notions. I am no more a Darwinian than I am an Einsteinian, a Newtonian, a Lavoisieran, a Galilean, or a Hawkingian. Strange, strange terms...

Amino Acids

In this section, my opponent asks me a question which seems to me that he actually answers himself in the text though he didn't recognize it. Given that certain natural processes seem to create amino acids in both their L and D (right-handed and left-handed chiral) forms, and that modern life only seems to use the L forms, he asks what mechanism could have done this?

Now I'm certainly no biologist, and my knowledge in these matters comes mainly from what I can research on the internet (I can't remember the last time I actually sat down and read a book, must be several years now; shame on me!) and what I can figure just using reason and logic. But when Livingstone himself says: "When L and D amino acids are together, then they are detrimental and toxic; they make the process of protein folding most difficult." it seems to me that your answer is right there.

If mixing the two types is indeed toxic (and I'm merely taking your word for it that it is; I have no idea) then it would seem that as living things were developing from non-living things, the only ones who could possibly "make it" were the ones that just happened to use only the one type or the other.

Given a solution of both and simple random inter-mixings, it stands to reason that while the majority would be a mixture of both, there would also be those at the ends of the spectrum that only managed to pull together one type or another. Though they would certainly be in the extreme minority, given that (as you implied) only they could actually live and reproduce, they would naturally and necessarily come to dominate. This is just plain old natural selection at work. Perhaps I'm missing some sort of nuance here?

But besides my amateurish speculation, there is actual work done by actual scientists on the matter that can be examined if one wishes. I went to PubMed ( http://www.ncbi.nlm.nih.gov/pubmed ) and entered "amino acid chirality biogenesis" to see what was there. I found 24 papers discussing the topic including an interesting one called "Punctuated Chirality".

Now, all I'm able to do is read the abstracts; I have no idea how one would get a hold of the text of such papers. But from what I've seen I haven't found anything that indicates that the current state of life is impossible by way of natural processes simply because the early Earth may have had both types of amino acids available to build from. Again I may be missing something, so I hope my opponent can fill me in.

Protein Primary Structure

In this section, my opponent introduces an argument from improbability. This is certainly a valid way to support his position, and I would agree with him that many cases where something that is very, very improbable is just as good as saying that it is impossible. The problem I often encounter with these sorts of arguments, however, is that they often completely misconstrue the actual improbabilities involved, and thus come to a false conclusion that the improbable event in question is indeed next to impossible. I believe the argument used here to be yet another example of this.

Even though many proteins are massively complex in their actual 3-D molecular structure, in terms of how these proteins are represented in the genetic code they are simply long strings of the four nucleotide bases. To ask how the proteins that living things utilize could become so complex, then, is to ask how the genetic codes themselves can change in order to build longer, larger, and more complex proteins.

As my opponent is probably already aware, the mechanisms which allow DNA to change are mutations. There are mutations which substitute one nucleotide for another, mutations which delete or add single nucleotides, and mutations which copy and repeat whole sections of DNA from short stretches to whole genes, whole chromosomes, and even entire genomes (the last being known as polyploidy). since these types of mutations are known, observable, and actually observed, it seems strange that my opponent would imply that these mechanisms to increase the complexity of protein building DNA sequences (and thus the proteins themselves) is somehow not well known as well as their actions being improbable to the point of practical impossibility.

What I think my opponent is actually arguing by implication here is the following:

• Because modern living things often require very complex proteins to function and could not survive without them, that very early life forms (down to the very first ones) would have also required these very same complex proteins.


• Since they couldn't have lived without them, these proteins could not have had the chance to evolve.


• If they could not have evolved, then they must have either fallen into place completely randomly or have been put into place specifically by the Grand Old Designer.


• Finally, since the chance of these exact proteins having fallen together randomly as they are is small enough to be effectively impossible, this gives good evidence for the necessity of said designer.

Have I got that about right, Livingstone?

But this is exactly the kind of misconstrued argument from probability that I spoke of earlier. While I would grant that some terribly complex proteins would probably never just fall together in a completely random fashion in order for the first (or any subsequent) life form to arise, they don't need to; the actual answer to the problem is one that my opponent skipped over due to a bad assumption.

This bad assumption (for those of you who haven't latched onto it already) is that just because modern life forms may absolutely require certain very specific and complex proteins in order to live, it most certainly does not mean that early life forms also needed these same specific proteins.

Imagine if you will, some population of early life forms going about the business of living using much simplified chemical processes and much simplified proteins. Through some random mutations, their primitive genetic material changes during replication, and their offspring now code for and build slightly different proteins. These will naturally run the gamut from less complex than the original, to equally complex but still different to the original, to more complex than the original. Also, like every other mutation, some will be detrimental to the organism (either causing immediate death or simply making them less efficient at competing for resources), most will be neutral, and some changes will in fact be beneficial. Natural selection will generally weed out the detrimental changes, and cause the beneficial ones to spread throughout the population and probably eventually dominate it.

In a similar fashion, living things undergoing evolutionary changes often change to specialize to certain environments, conditions, and processes. If this specialization also provides a selective advantage, then it too will probably come to dominate the population.

What we have here is a plain (even Darwinian) model of how living things can go from using simpler proteins early on, to eventually using more complex proteins later, and even specializing to the point that the more complex proteins are no longer just optional and only slightly more optimal, but are actually necessary for the organism to continue to live.

Now again, I really have no idea what specific proteins come from specific earlier proteins and by what specific mutations, nor do I know the specific chemical and genetic compositions of those early life forms. But the possible pathway to this end by completely known and naturalistic mechanisms is clear.

If my opponent still wishes to argue that this process that I have only broadly outlined is still much too unlikely or even impossible, and thus an intelligent designer is necessary, then I would ask at what step in the process does the impossibility lie?

Metabolic Pathways

Since this post is already pretty long and involved, and since it is taking me way too long to get this written and posted (and not posting is boring for our spectators). I ask that we forego this particular point for now, and concentrate on what has already been dealt with. I imagine that my response to it at this point would be very similar in nature to my other responses anyway. We can, of course, return to it later once we've thinned things out a bit.

Other Factors

I smiled at the inclusion of this point. Yes indeed there are other factors to be considered, and consider them we shall as long as time and space permit and everyone is still interested. I trust that your other factors will be met satisfactorily by my other responses.


And this concludes the end of round one. What surprises, insights, and possible lameness will round two hold? Stay tuned and keep watching this space...

Daniel "Theophage" Clark

Debate: Intelligent design is necessary to account for life on Earth

I will begin this debate on Intelligent Design and the origin of life with the following statements, arranged thus:

1. Protein Primary Structure
2. Metabolic Pathways
3. Amino Acids
4. The Genetic Code
5. Other Factors

Protein Primary Structure

All biologically active organisms demand functional proteins. We hold that the first life form that arose is no different: all empirical evidence suggests that life demands proteins. How, then did extremely complex protein tertiary and primary structures arise through unintelligent processes? Certainly, shorter proteins could feasibly arise through unintelligent processes. However, it is most improbable that longer and more complex proteins (for example, those belonging to the alpha/beta classes) could arise through unintelligent and chaotic processes.

In explaining a hypothetical model whereby such a/b class proteins can arise, we must take several things into consideration:

“There is a key difference between the evolution of organisms vs. the evolution of proteins: the current model of evolution of organisms has the absolute requirement of reproduction of organisms and, thus, all present-day organisms ultimately come from one common ancestor organism. However, the evolution of proteins, therefore genes, does not need to follow the evolutionary path of organismic reproduction. Rather, the evolution of proteins is directly related to improved, unaltered, or diversified molecular functions, and the protein function is directly related to protein structure.”

[Choi, “Evolution of Protein Structural Classes And Protein Sequence Families.”]

Is there any feasible paradigm for the evolution of alpha/beta class proteins?

Metabolic Pathways

To examine whether a complex biochemical system can evolve through natural selection, one must simply understand what the ultimate function of that system is.

In the case of glycolysis, a metabolic pathway that is a sine qua nons to all living organisms, the ultimate function is the net gain of two ATP molecules from an ADP molecule. To achieve this function, a series of small-scale reactions must take place.

Now, in order for such a reaction to be able to evolve in a cellular organism, every step along the way must have an advantage (or at least not be detrimental), or else it would be weeded out by natural selection.

In the case of glycolysis, the cell invests an ATP molecule to make glucose-6 phosphate. This first step in glycolysis is entirely counterproductive to the cell; that is, until an enzyme comes along and makes use of the glucose-6 phosphate.

Thus, such a cell, valiantly attemtping to evolve the process of glycolysis through natural selection, would be weeded out by natural selection, as it sacrifices an ATP molecule for no functional reason; this means the cell would waste energy that could be used for various metabolic processes.

How far then, could life advance without glycolysis? True, the first cells did not depend on glycolysis, but this demonstrates the difficulty of metabolic pathways evolving.

Amino Acids

All life is composed of L amino acid proteins. The Miller-Urey experiment demonstrated that amino acids can arise through unintelligent processes; however the amino acids that did come about in the above experiment were composed of both L and D amino acids. When L and D amino acids are together, then they are detrimental and toxic; they make the process of protein folding most difficult. I ask how the first life arose managed with L and D amino acids all in one configuration, and how it eventually got rid of D amino acids and kept only L amino acids? What kind of process or mechanism would this entail?

The Genetic Code

Lastly, one must ask how DNA and RNA could have feasibly formed; how the entire processes of replication, translation, and transcription formed. The existence of a genetic code is perhaps one of the most devastating arguments against Darwinians who believe life can arise through unintelligent processes.

Other Factors

There are other factors which must be taken into consideration when one deliberates on the origin of life, of course, though I will not attempt to outline them here.

Livingstone M.