Theophage's Third Post

For those of you following along, I hope this exchange has managed to keep your interest so far. I think my opponent's last post was very good, and I think we are beginning to get down to the nitty-gritty of the disagreement over intelligent vs. unintelligent design. I see only better and better things ahead for this debate, so please spread the word to your friends and enemies alike and leave us some comments as to how we're doing.

Ideally I'd like to get some sense of just how many people are reading this and following along. (If we wanted no one else to see it, we could have done this all by email.) So even if you have no comment other than "I'm obviously cool and hip because I'm reading along," we'd love to see that.

The ET Hypothesis

If we examine the history of the intelligent design movement, it is clear that there is almost exclusively religious motivation behind it. Proof of God is sought in His creation, and intelligent design fills that need nicely. I daresay that (nearly) all of the prominent names in the intelligent design movement come straight out of earlier creationist movements. I hope my opponent is not trying to deny this easily demonstrated fact.

It is also easily demonstrable that there was and is a definite push to disguise intelligent design as non-religious for the purposes of including it in public school curricula. These intentions were made clear by the Discovery Institute's leaked "Wedge Document" and was decided definitively in the Kitzmiller vs Dover trial.

So while it is technically true that intelligent design does not necessarily point to God, to ignore the obvious cultural and historical context would be like someone being accused of using racial stereotypes when talking about fried chicken and watermelon and responding "That isn't a racial thing, lots of people like both watermelon and fried chicken..."

Is it a terrible thing to say "It could be aliens or whomever"? No, it isn't a terrible thing. I even understand it on a certain level: If we can scientifically prove designed features in life, that information may or may not even be able clue us in to the identity of the designer. But given that the obvious motivation behind intelligent design research is to reconcile God and science, it seems odd that one would go to such great lengths to then deny we are talking about God. Terrible? No. Curious? Quite.

Anyway, I think this tangent has run it's course, and this will be the last I have to say about this matter. (Though I reserve the right to still use the term 'Grand Old Designer' because it tickles me.)

Design as Explanation

In response to my assertion that he has been putting forth arguments from ignorance, my opponent wrote that his reasoning is actually:

"(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."

Now I will grant that this is a valid form of reasoning, and one that is used in science all the time. If theory X explains A and B, but has no explanation for C, while theory Y explains A, B, and C, then of course theory Y is preferred and considered the "correct" view (until possibly replaced by better theories later, of course). But does intelligent design really offer a better explanation? I say no, I don't think it offers any explanation at all.

My opponent outlined the argument from ignorance thusly:

"we do not know of a Darwinian mechanism for X, therefore ‘an intelligent designer dunnit.’"

We both agree that this is a poor argument and as an explanation provides us with absolutely nothing. It is simply the 'God of the gaps' argument I brought up earlier with 'God' replaced by 'an intelligent designer' (remember, it could be aliens...)

So his actual argument has to be better than this, right? Intelligent design according to his argument has to explain more than the argument from ignorance, right? Well, let's look at what the intelligent design explanation actually gives us:

• What is the origin of the genetic code? ‘An intelligent designer dunnit.’


• What is the origin of the homochirality of amino acids used by life? ‘An intelligent designer dunnit.’


• How could "longer and more complex proteins (for example, those belonging to the alpha/beta classes)" arise? ‘An intelligent designer dunnit.’


• What is the origin of the complex metabolic pathways involving glycolysis? ‘An intelligent designer dunnit.’


• Why do some viruses use RNA, some use single strand DNA, and some use double strand DNA for their heritable material? ‘An intelligent designer dunnit’ that way.


• Why is this protein or this system or this anatomical part used instead of this other one? ‘An intelligent designer dunnit’ that way.


• Why did the intelligent designer choose to do it this way instead of that way? ‘An intelligent designer dunnit’ that way.

I'm sorry Livingstone, perhaps I'm just a moron, but I'm not seeing any explanatory difference between what you are arguing and simply a Grand Old Designer of the gaps type argument from ignorance. Can you please explain better?

It would seem that I could turn around and answer all of those above questions with "Nature dunnit" or "Unintelligent 'Darwinian' processes dunnit" and it would contain exactly the same explanatory value (i.e. none). And yet my opponent assures us that "the intelligent design model best explains X". How can this be?

A real scientific explanation is one that gives us additional information either about a previously unknown fact or process, or links previously known facts or processes together in newly discovered ways. An explanation can hardly be considered good or even adequate unless it increases our knowledge about the explained thing somehow. How does the idea that life is intelligently designed increase our knowledge about life and how it works, even one bit?

Again. I simply don't see it.

What's worse, imagine if other branches of science used this same type of reasoning. Why do atoms of one type combine readily with another type but not with a third type? Should we have not learned about electron shells and orbitals (or even the periodic table itself) and simply stuck with "the designer made them that way"? No, of course not.

The fact is that learning about the physical reasons why some things are the way they are increases our knowledge about the world. Saying that they just are that way or that they were just made that way by an inscrutable being increases nothing and in fact inhibits the gaining of knowledge.

So no, even if intelligent design is true (and my opponent has not yet shown that to be the case), it still is not any kind of a "better explanation".

Bad Probabilities

Earlier in this debate I argued that my opponent is (and generally all other intelligent design proponents are) using a bad argument from probability when talking about the likelihood of a particular protein or whatever forming by chance. To illustrate his bad reasoning, I used the example of dealing out an entire deck of cards (jokers included) and showing that even though the probability of that exact sequence of cards coming up is just this side of impossible, that does not mean a miracle occurs every time we deal out the cards. The difference is in having a goal sequence that you're trying to match with the random process.

Livingstone came up with a fairly clever response to this, and compared my problem of probability with a commonly used argument for common descent, that of shared ERV sequences. Briefly, the inserted DNA sequences from retroviruses in the human genome follow a certain pattern of placement, and a very similar pattern is also found in the chimpanzee genome. These ERV sequences aren't functional, so they aren't subject to selection even though they are still passed down by normal heredity. The probability that the specific pattern and placement of these ERVs in the human and chimpanzee genomes is the same is so terribly, incredibly small that it isn't considered to be possible by chance, and thus common ancestry is the explanation for why they are so similar.

My opponent says that if we use the reasoning of my critique, then the sequences aren't so terribly improbable at all, and thus I am undercutting my own position by using this critique. I can't have it both ways, right? Either it is or it isn't terribly improbable to come up with particular sequences and patterns. Well, as expected, my opponent is mistaken on this issue once again.

Protein formation by chance is analogous to dealing cards out on the table, and it is also analogous to ERV sequences accruing in the genome of a species by chance. As I demonstrated earlier, no miracle occurs in any of these processes, they are fairly straight forward. The only thing that would be terribly improbable is for these processes to end up matching a particular pre-selected goal.

In the case of ERVs being used as evidence of common descent, it isn't the pattern of ERVs in either the human or chimpanzee genome that is terribly improbable, it is the comparison of the two; that's the key.

To give another card example, take one deck of well shuffled cards and deal them out onto the table. Yay! They have some particular arrangement without invoking a miracle, yes? Now, grab another deck of well shuffled cards and deal them out onto the table in a line below (or above, I'm not picky) the first. What are the chances that both are the same arrangement? That's right, it's exactly the number I calculated earlier: about 1 in 2 * 10^70. The sequence of the first deck is the goal that the second deck is trying to match, and the chances of that are indeed effectively impossible without some mechanism to make them that way.

This is what we are talking about when we use the ERV argument. For the human genome to have a pattern of ERVs by chance is not impossible. For chimpanzees to have a pattern of ERVs by chance is not impossible. For both species to have such a similar pattern purely by chance is indeed impossible.

Similarly, for random DNA patterns to code for any particular complicated protein you can think of is next to impossible, but only because you are trying to compare the result of the simple unintelligent evolutionary process with a pre-determined goal. For just any complicated proteins to arise just by simple unintelligent processes, by contrast, is no more improbable than just dealing out a deck of cards. Are we clear on the difference now? Remember: bad probability arguments are bad.

Amino Acids and the Genetic Code

My opponent has been asking me some terribly difficult and specific questions about biochemistry. Even though before the debate began I specifically said that I had no answer to these types of questions, since we agreed that "I don't know" is a boring answer, I tried to oblige and give my best responses to them. As my opponent has shown, they just don't hold up to scrutiny; no big surprise there. We both know that there simply aren't any answers to these questions in current scientific knowledge.

So why was my opponent asking me these questions? Ostensibly, it was to support his argument that while mainstream science had no good explanations for these things, that intelligent design does have explanations, and thus an existent explanation is clearly superior to a non-existent one. But as I'd shown above, his explanation consists of essentially "the Grand Old Designer made them that way".

While I agree that it would be perfectly possible for an intelligent being with the appropriate technology to do so, that again fails as an explanation because it gives us exactly zero additional knowledge about these processes and life itself. Should the fact that it is possible for an intelligent being with the proper resources to cause it to rain over Battle Creek, Michigan mean that we should then accept that as the reason it is raining on my roof right now? Or should there be some criteria other than mere possibility to determine what actually is the cause of something? Possibility is a necessary but not a sufficient criteria for determining cause. This is an important fact.

As I'd written earlier in this debate, in order to support the claim that intelligent design is necessary for the existence of life on Earth, it isn't sufficient to simply show that an intelligent being could have done it, it has to be shown that it couldn't have happened any other way. Surely we all agree that 'possible' does not equal 'necessary'.

Consequently, Livingstone has to do more than simply show that mainstream science doesn't currently have explanations for these things in order to support his case, he has to show that they cannot possibly have them. Only if that is true can we then regard intelligent design as necessary.

And unless I'm totally missing something (which is not an impossibility), he simply has not done this so far. "Don't know how" in no way equals "can't be done".

Bringing up the nylon bug

My opponent said, "I really don’t know what my opponent’s reason was for bringing up the evolution of nylonase." I try to make my points as clear as I can so that everyone can follow along, but perhaps I failed to do so here. I will try to explain again:

The information I had about the nylon-eating bacteria was that it's ability to digest nylon was caused by an earlier gene duplication followed by a particular frame shift mutation in the duplicated gene. Why is this relevant? Because it is an example of an entirely new protein consisting of hundreds of amino acids coded essentially out of nowhere by mutation alone in a single step.

A frame shift mutation is one which changes the genetic reading frame such as a deletion or insertion of one or many nucleotides. The genetic material codes for amino acids in groups of three nucleotides at a time, so that every three 'letters' in the gene spells out one amino acid 'word'. If you delete or add a single nucleotide to the gene, everything after the mutation gets shifted one 'letter' one way or the other. This means that all of the amino acids coded for after the mutation to the end of the gene are completely different; it isn't just a matter of the same protein with a couple of amino acids different, it becomes an entirely new protein.

My point in bringing this up is that this is one naturalistic, unintelligent mechanism for coming up with entirely new proteins all at once instead of in a stepwise fashion, where each step has to provide some sort of selective advantage in order to be carried on to the next step. Can we all see the significance of this? If not, I'll try to explain again next time.

Now I was rather unpleasantly surprised to find that this isn't what happened in this particular case after all when I read the Wikipedia article. The original paper on the nylon bug by S. Ohno in 1984 was incorrect. But as disappointed as I am that this wasn't the actual case with this particular organism, my point still stands just as firm. New proteins most certainly can be created by unintelligent frameshift mutations in which the new protein may be totally unlike the protein that the unmutated gene originally coded for.

Other Comments

With the main points in the argument now addressed, I'd like to make a few comments on some other things I found in Livingstone's last entry.

Regarding the nature of the ability to digest nylon, my opponent wrote (bolding is mine):

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 ability was already present?

Yes, the ability to digest other materials for food was indeed present, but what made this special was the new ability to digest a new food source. I realize that you've already said that you don't dispute that new functions, information, and complexity can be added by mutation and selection (like many of our creationist friends would dispute), so why are you downplaying the fact that this function is a new one?

His reasoning is apparently thus:

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.

I think even we in the unintelligent design camp would be surprised if it would take "trillions upon trillions of mutations to eventually evolve a novel function". Livingstone makes it seem like we require mutation and natural selection to plan ahead many, many steps in advance in order to explain life, but that fact is that we simply don't.

Right after this section, my opponent wrote this extremely curious sentence:

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

It was? 200,000 years ago? How in the world did you come up with that oddly specific bit of information? And how do you know that the Grand Old Designer(s) isn't at work today?

Speaking of the hypothetical designer(s):

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.

Which is odd because you also said that the genetic code is a clear indicator of intelligence, so presumably these hypothetical aliens are alive without having any kind of genetic code? No known way to store heritable traits or produce proteins required for a body of some sort? This means that they would have to be a form of life completely different from anything we know today, indeed, possibly even something that we may not even perceive as alive at all.

Now if we were talking about a supernatural living 'spirit' (say that a God would have), that idea makes a little more sense. A spirit body presumably does not require any sort of molecular machinery or genetic code. But why would these hypothetical alien designers make a form of life so different than their own, when apparently whatever they have works pretty well? Curiouser and curiouser...

And speaking of genetic codes:

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.

Well of course one's position is strengthened if one is begging the question, that's the whole point of using logical fallacies: to give one's position an unwarranted advantage!

But I don't think that is necessarily what you are doing here. What we do have is an inductive argument of the form:

1) All known languages are the product of intelligence.
2) DNA is a language.
3) Therefore it is most likely that DNA is a product of intelligence.

Even though "most likely" still falls short of what my opponent needs to show in this debate (that intelligent design is necessary to account for life on Earth) I would grant that this would be pretty good evidence in favor of intelligent design were it's premises indeed true.

Unfortunately, the argument here fails because premise 2 fails. DNA and the genetic code is only a language in the metaphoric sense. Note my use of the metaphors of 'letter' for nucleotide base and 'word' for nucleotide triplet which codes for an amino acid above.

Even following the mathematical relationship noted by Zipf doesn't make something a language; Livingstone's reference above was misleading. From this article: http://en.wikipedia.org/wiki/Zipf's_law

It is not known why Zipf's law holds for most languages. However, it may be partially explained by the statistical analysis of randomly-generated texts. Wentian Li has shown that if you create a document where each character is chosen randomly from a uniform distribution of all letters (plus a space character), then the "words" in this document also follow the general trend of Zipf's law (appearing approximately linear on log-log plot). This suggests a partial explanation for why Zipf's law might hold for most natural languages (although the law holds much more strongly to natural language than to random texts).

The Zipf relation is also found in many other non-language contexts such as the stock market. So to conclude that just because something follows that particular relationship that it must therefore be a language is demonstrably false.

Cutting it Short

Once again it has taken me way too long to finish a post, so I'm going to cut this one short here. Once again I would like to acknowledge that while I haven't addressed everything in my opponent's last post, I feel I have addressed the major issues. But if there is something important that Livingstone feels I should have addressed but didn't, please let me know and I'll make sure it is one that definitely I include next time. I don't want to avoid any important issues because for one it is dishonest in a debate, but also because it is unfair to our audience. And you guys know I'm doing all of this for you, right?

Daniel "Theophage" Clark

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