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