Theophage's 4th: New Directions and Old Repeats

What's all this about then?

Several times through this debate, my opponent has assured us that intelligent design is a better explanation for life and the universe. From his most recent post:

the theory of intelligent design holds that certain features of the universe and biosphere are better explained by the actions of a rational agent than purely undirected processes.

The first thing I notice about this statement is that it is actually irrelevant to the debate at hand. FirstFreedomFighter and I tossed around several vague debate proposals before settling on the exact proposal which is posted on the right side of this blog for all to see: "Intelligent Design is necessary to account for the existence of life on Earth."

The problem here is that regardless of whether intelligent design is true or not, or whether it is a better explanation or not, the role FFF accepted in this debate was to affirm that intelligent design is necessary to account for life on Earth. I mentioned this important detail several times so far including in my last post, but he hasn't seemed to address this most glaring incongruity at all. These things are most certainly not the same.

My opponent wrote specifically:

Throughout this debate, my central argument is not merely ‘mainstream science has not explanation for X, therefore goddunnit.’ My argument is based upon a clear and conscience acknowledgement of the fact that the intelligent design postulate does not hold that intelligent design is absolutely necessary for the origin of life or its ultimate diversification, but rather that certain features of the biosphere are more adequately explained by the intelligent design proposition.

And yet that is absolutely not the debate proposal we agreed upon.

So I ask you, Livingstone, are you going to somehow move logically from "best explanation" to "necessary to account for" or do you want to concede the current debate proposal and try again with the new proposal: "Intelligent design is the best explanation for life on Earth"? I assure you that I will be a most gracious victor if you wish to concede. You do see the difference between the two proposals, right?

A Better Explanation?

The second thing I notice in the passage quoted above is, of course, the claim that intelligent design actually is a better explanation. This is an area where Livingstone and I clearly disagree, but I think we need to come to some kind of agreement about what constitutes a 'better' or even a 'good' explanation before we can determine which of us is correct. There is not much point in trying to compare apples to oranges, right?

In my last post, I tried to outline some differences between a good explanation and a poor explanation. Things like how a good explanation increases our knowledge about things, how it links to other known things, etc. I trust my opponent will let us know if he finds any of these criteria objectionable, or if he has any to add that I haven't covered.

Once we have established a common set of criteria for what makes a good explanation, then it is a simple matter to determine which explanation is better than another just by adding up all the 'pros' and subtracting the 'cons'.

As I'd granted earlier, of course, there are many things about how life arose and changed over the eons that the biological sciences simply cannot explain at the present time (using known unintelligent natural processes). That means that for mainstream science's case, what we have in some instances is a known agent (Nature) and some known and unknown processes involved.

For intelligent design's case, we have essentially the reverse: an unknown agent and (as Livingstone's examples indicate) some possible known processes. I say 'possible' because we simply don't know if these processes were used or not. Only additional evidence of these processes (like the ruins of some billion year old biology labs at the bottom of the sea, for example) could let us know if these processes were indeed used.

Notice that in both cases we have a huge, glaring unknown. How does simply trading one unknown for another make for a better explanation? To my way of thinking, it doesn't and it can't.

"Nature did it" is no more of a good explanation than "the Grand Old Designer did it"; both are far too lacking in informative value to be useful as explanations let alone is there enough there to say that one is somehow better than the other. So I guess I'd like to hear my opponent explain why he thinks one truly is better than the other. Specifically, Livingstone, how does trading one unknown for another make for a better explanation?

For illustrative purposes, let me put both of these together:

1) Mainstream science has no explanation for X,
2) Intelligent design does offer a mechanism for X,
3) Therefore the intelligent design postulate is a more adequate explanation for X.

but:

1) Intelligent design has no known agent to implement the process involved in X,
2) Mainstream science does offer a known agent to implement the process involved in X,
3) Therefore mainstream science's postulate (unintelligent nature is responsible) is a more adequate explanation for X.

I also "fail to see any flaw in my logic and rational[e]". That's why we're doing this, to point out our flaws.

Mainstream Science

The more astute of our readers (all five of you) may have noticed in the first syllogism above that I replaced my opponent's wording with "Mainstream science". Why did I do that?

The point is one I would like to make perfectly clear: Intelligent Design is not mainstream science; it is not part of the current fields of biology, chemistry, or physics. This is an important fact that we must seek to explain somehow.

Those less stable and more prone to tinfoil sombreros among us, assure us that it is because of a great conspiracy among scientists and science in general; "The Man" is keeping down the truth for nefarious reasons and simply won't allow dissent. To someone who believes this way...well...I really don't know what I or anyone else could possibly say that would convince you otherwise. In fact, I think we have one of our agents heading to your location right now to straighten it all out for you...

In reality, the reason is because at the current time there simply isn't sufficient evidence to conclude intelligent design in life. Period.

But this is completely at odds with what my opponent is trying to convince us of. To hear him tell it, the evidence is both blatant and plentiful. So we are left with a choice of what seems to be more probable: either virtually every expert in the appropriate fields of science are somehow blissfully ignorant of this overwhelming evidence of design, or the case for intelligent design is simply not as obvious or as well evidenced as Livingstone thinks it is and is arguing here that it is. I'm pretty sure that the former is much more likely than the latter.

My List of Questions

In support of my argument that intelligent design isn't a better explanation at all, I gave several example questions and applied Livingstone's reasoning (or a close facsimile thereof) to them to show that they didn't offer anything better than a designer-of-the-gaps argument that he swears he isn't using. He gave some answers to these which I think are worth examining to again try to understand how (if at all) the intelligent design proposal gives us any more insight or actually is a better explanation. Again, I think his reasoning fails, and I would like to show why point by point:

* What is the origin of the genetic code? Ribosomal engineering techniques explain the origin of the genetic code better than undirected processes.

Well, that is certainly a possible explanation, but again you have no evidence of an intelligent being utilizing those processes, nor any evidence that those processes in particular were used other than to say that it simply could have been that way. How are those unknowns any more advantageous than talking about an unknown natural process that didn't require an additional intelligent agent to work them?

* What is the origin of the homochirality of amino acids used by life? What’s the problem with a designer using chiral synthesis pools and chemical bonding breakage technology?

Again, we have possible processes, but what is the evidence that these processes were used? Where is the archaeological remains of the facilities in which these were done, or of the intelligent beings which did them? None? What about molecular evidence? Is there a particular molecular signature left when these processes are used as opposed to any other which may accomplish the same job? (Like how in my example of the crystal skulls, the trace physical remains of the process helped determine what processes were used to create them.)

Again, how is an explanation with a huge unknown like this better than an explanation with a known agent (nature) and a different but unknown process?

Oh, and you asked earlier if there were any other known processes which would either produce only a single enantiomer instead of both or be able to sort only one type from a mixture. Now this may be me being naive again, but doesn't the chemical processes of life itself do that now? So certainly, processes are known which do this which don't require an immediate intelligent agent to do them, right? Like in plants, bacteria, etc? So to say that no such processes exist is patently false.

* How could "longer and more complex proteins (for example, those belonging to the alpha/beta classes)" arise? Directed enzyme evolution coupled with recombinant DNA techniques.

Again, it is absolutely possible that an intelligent being or beings put them this way using these techniques, but possibility does not make either probability, likelihood, or necessity. That is where your reasoning falls apart.

As I'd said in my last post, the fact that it is possible that the rain falling on my roof was not coming from a natural process, but by an intelligent agent actually dribbling water on my house does not somehow make it more probable, likely, or necessarily true, even if we didn't know the natural process of how it does rain. Yet this is exactly what you seem to be claiming about these other phenomena. What is the difference and how can we tell?

* Why do some viruses use RNA, some use single strand DNA, and some use double strand DNA for their heritable material? Degenerative processes dunnit.

+5 points for style, but -100 for substance. The point I was making here is like the rest hereafter, so I'll re-explain in the next one:

* Why is this protein or this system or this anatomical part used instead of this other one? I don’t get the point of this argument or any of the arguments entailed below this one.

I try to make my points as clear as possible, but I am only human. As I'd said in my last post, part of what makes a good explanation 'good' is the additional information it gives us about the phenomena. A good explanation doesn't just tell us what happens, it tells us why it happens this way and not a different way.

Why doesn't it rain gumdrops? Because huge gumdrop seas don't evaporate and collect into gumdrop clouds suspending little gumdroplets in the air which combine together at nucleation sites and fall to the ground as fat gumdrops once they get too heavy. But all of this does indeed happen to water, which is why it rains water.

If we explained rainfall as simply the Grand Old Designer dropping stuff on us from above, then there is absolutely no reason why it couldn't be gumdrops other than "because that's just not what the Grand Old Designer chose". A good explanation tells us why this and not that.

If intelligent design really is a better explanation for these processes as you say it is, then it should give us some insight into all of the above questions: why this instead of that, why is this virus using RNA and this one using DNA, etc. I certainly expect the naturalistic, unintelligent explanations to give us this kind of detail once they are found as well.

But what we see is that adding an intelligent designer to the mix does not give us any of this additional information at all. That is my point. Your explanation gives us no more information than we could get from simply saying "The Grand Old Designer dunnit".

And because of this, you have absolutely no grounds to claim that it is a better explanation than a standard Grand-Old-Designer-of-the-gaps argument. Are we clear on this point now?

Bad Probability Arguments Are Still Bad

I want to thank my opponent for the concession on the particular bad example that he used, but it wasn't just the example I had issue with, it was his entire mode of reasoning which he still seems to be using. He says that you can still use a probability argument if we're talking about matching a goal, and that the goal of life is functionality. But does that really work?

First, simply declaring that a goal exists does not actually make it a goal. It is a goal only in a metaphoric sense; neither the universe, nor the planet, nor the molecules themselves care if they are functional or not. The simple fact is that functioning life reproduces and makes more functioning life, and non-functioning life (if it can be non-functioning and still live) does not. That is simply an observation about what obtains, not any kind of evidence of a goal.

But even if I grant that it is the goal of life and the processes of life, how then does one calculate the probability (or improbability) of reaching this goal? It is Livingstone's contention that the improbability of this is a de facto impossibility, yet he has to show this to be true. One doesn't just get to assert it and leave it at that.

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

And not only am I not going to let my opponent simply assert its improbability, I'm doubly not going to let him totally beg the question as he does here:

To put this in the form of card-playing:
Let the royal flush be functionality, and all other card sequences redundant, non-coding regions of DNA. What is the probability of the royal flush being obtained? Next to nil, and this is analogous to my argument on protein formation.

So if we assume that the probability of functionality is a rare thing, like being dealt a royal flush, then naturally we must conclude that functionality is a rare thing like being dealt a royal flush, right? Am I really the only one seeing this here? Bad probability analogies are also bad.

Please show us how you figure that functionality is rare. Then we can see whether or not your reasoning is good and your conclusion is correct. Remember, functionality is not just a matter of the individual protein or other molecule itself, but the system the protein finds itself in: Protein A may be perfectly functional in environment X, but fail to do anything in environment Y. How you're going to work that into your calculations should be interesting.

Protein Primary Structures Again

"You keep using that word. I do not think it means what you think it means." - Inigo Montoya

You keep using the term "protein primary structures". Not being as familiar with biochemistry lingo as you are, I didn't quite catch on in the beginning, but now that I have done more reading (and believe me, I have learned a lot since I began this debate with you, that alone makes everything worth it!) I find it more and more curious why you use this term the way you do. For example from your last post:

I believe I can demonstrate that my argument on protein evolution and probability does indeed indicate that there is indeed virtually no chance of protein primary structures evolving through Darwinian mechanisms.

and this:

I know of no undirected evolutionary mechanism (like Lamarckism or saltationism) which can offer a feasible model that would demonstrate how these protein primary structures arose.

For those of you who don't know, a protein's primary structure is the sequence of amino acids which make it up. This comes directly from the DNA sequence in the gene that codes for the protein. So when you are asking about how a particular protein primary structure evolved, what you are really asking is how the gene evolved. Why not just say that? Is there some difference here that I'm missing?

Yet "Darwinian mechanisms" are all about how genes evolve, or rather how traits evolve, and the neo-Darwinian synthesis in biology takes that to the genetic level including non-expressed regions of DNA. How can you possibly claim that there are no such mechanisms or that such mechanisms cannot account for what we find?

Granted, we may not know the evolutionary history of a particular gene, or of the particular process which makes use of the protein encoded by it, but that is a very far cry from 'no known mechanisms' which is what you claim and especially from 'no possible mechanisms' which is what you would have to show in order to support our agreed upon debate proposal.

There is a lot that we do know, and it is my understanding that it is because of that knowledge that makes it more likely that these same processes account for all genes and all proteins used by living things.

Nylonase ad Nauseam

Livingstone postulates that there is probably a barrier of non-functional structures in the case of the EPSP synthase which accounts for why it could not have evolved, whereas there must not have been any such barriers in the case of the nylonase which was produced by unguided evolution in the case of the various nylon-eating bacteria. This may, or may not be true.

He referenced a paper which seemed to indicate this, but I'm not totally sure given that I didn't make my way completely through the paper. (And by not "completely through" I mean I skimmed it quickly, ran into a bunch of stuff that made little sense to me, and then quit...) Clearly mainstream biology doesn't know how this particular protein, its associated gene, or the system that uses it evolved. But I'm fairly certain that the point of the paper wasn't that it couldn't have evolved, so for my opponent to use it this way is misleading at best.

I'm going to try to plow through that paper again, and I encourage you the readers as well as Livingstone himself to go through it and see if it really supports the case that he postulates that it does.

I explained why I thought the case of the nylonase is significant, but still my opponent says: "Again, I fail to realize how this applies directly to this conversation on protein evolution." Let me run though this one more time:

It is one thing to see obvious evidence of simple evolutionary change in a gene. If we look at the difference in the sequences for cytochrome C across species, we can see that while evolution has made a few changes here and there over the eons, the protein itself is fairly highly conserved (meaning it's overall structure and function doesn't change much). The exact mutations between species and other groups are fairly easy to place both in type (what changed) and in time (when in evolutionary history it happened). But like most things, not all cases are that simple.

It is possible for an entirely new protein to essentially "come out of nowhere" and not be similar at all to its predecessor. This is much more likely in the case of a duplicated gene, where an unchanged copy still remains to do the job, but the new copy is free to provide new function. The mechanism for this is not some wild imagining of my particular biochemical ignorance and naivete, but an actual known and studied mechanism, that of a frameshift type mutation.

While the gene having undergone the frameshift is fairly similar to the original, the protein that it codes for is most certainly not. Some relevant links:
http://en.wikipedia.org/wiki/Frameshift_mutation
http://ghr.nlm.nih.gov/handbook/illustrations/frameshift

My point being that if this happens somewhere in the evolutionary history of life, then tracing back the original protein this new protein came from becomes exceedingly more complex, since now we're looking for something totally dissimilar. It could very well be that the resulting protein, if it has or finds a new function, has no similar functionality in any further slightly mutated form; Livingstone's barrier in effect. And yet it wouldn't need functionality in a close but different form in order to have evolved in this way.

Is this the case with EPSP synthase specifically? I really have no idea. But my point is that it is possible, and if there is a possibility, then the opposite claim (that there is no possibility) cannot be true. Livingstone cannot claim that there is no possible way for it to evolve when there is, and that is exactly what he needs to claim in order to show that the intelligent design of this protein is necessary as per our agreed upon debate topic. That is my point.

Do you see how this is relevant now? I'll explain again if you'd like, but I don't think it will look any different next time. I can only do my best.

Miscellaneous Critiques

Related to the above, Livingstone clarified his comment regarding the precursor gene to the evolved nylonase gene:

The potential to evolve the functionality of synthesizing nylon was already present, as it did not require natural selection to ‘browse’ through an endless array of non-beneficial protein primary structures.

But what does that mean that the 'potential' was present? What it means is simply that it is possible to arrive at the derived gene from the original gene by way of normal unguided evolutionary mechanisms. Okay, I'll accept that.

But that last part is rather curious (and probably false). Where in any paper does it say that the mutated gene was arrived at in a single step? That would be the implication if there was no browsing alternatives involved. How do we know that that other, non-functional mutations of this gene weren't tried first? Is my opponent just assuming this?

Did the bacteria somehow "know" that they had to make this particular mutation at this particular place in order to capitalize on a new food source? Absolutely not. It is almost assured that many mutations were tried and the right one came up and was therefore used; that's the way evolution works.

Am I totally misunderstanding what my opponent is saying here? Because it seems blatantly and demonstrably wrong to me.

We don't even have to talk specifically about the nylonase case in order to to see a similar process at work. Here is a link to an article about The E. coli long-term evolution experiment done by Richard Lenski: http://en.wikipedia.org/wiki/E._coli_long-term_evolution_experiment

During this experiment, certain groups of the bacteria he was using developed an ability to eat citrate. This took place after thousands of generations, and actually required two separate mutations which (apparently) were not beneficial without the other. And yet there it is, it happened.

Clearly over thousands of generations and millions of mutations, natural selection searched through many alternatives and chose those that just happened to be beneficial. there was no particular goal involved, the point of the experiment was not even to get them to eat the citrate. But mutation and natural selection don't operate with goals in mind. What happens to work simply gets passed on, and what doesn't doesn't. How can Livingstone say what he said above in light of this?

Let's look at this a little more abstractly: Let's say we have a sequence of numbers, like 0305821875. Now what Livingstone seems to be saying is that given the rules that we can change at random any number in the sequence, add or subtract numbers, or copy sections of numbers and repeat them (these being analogous to mutation), we somehow cannot start with the sequence given and end with something like 345677243457. Really?

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

Yes, the Grand Old Designer may have simply wrote 345677243457 with some intent and purpose in mind I'm not saying that isn't a possibility, but when you have no evidence of said designer, and when the known rules allow such changes to be possible, is it really the 'better' explanation? Not at all, and yet this is what my opponent wants us to accept.

Also in his last post, my opponent concedes to me a second time (apparently), but curiously says it this way:

I concede the point, that, using Zipf’s laws, DNA is a language.

I think he meant that he is conceding the point that just by following the Zipf relationship it doesn't make DNA a language, but he is, after all, only human and prone to mistakes. I hope all of our readers picked up on that and weren't too confused.

Regarding why the hypothetical alien designers used a genetic code for life (which my opponent claimed is sure evidence of intelligent design) while they themselves wouldn't have had one (since they wouldn't have been intelligently designed), he mentions a possible example in how prions transmit their heritable traits.

This is a perfectly fine speculation and I don't doubt that on some level it may be possible, but it still fails to account for why the designers would have chosen to make the life that they created and designed so different from the way they themselves work chemically.

Clearly whatever system they used was good enough to achieve sentience and technological sophistication, and have come about billions of years earlier in the lifetime of the universe, but then they for some reason decided to say: "...and now for something completely different". This is just the sort of additional information which I would think that a truly good explanation of life would provide; again, why is it this way instead of that way, which once again Livingstone's postulate fails to provide. How is it a better explanation again?

Finally, my opponent answered why he felt that the designer took his seventh-day rest about 200,000 years ago with the advent of Homo sapiens. We went over this a bit in private messages before his debate post appeared, and I told him how I felt that this seemed like simple anthropocentrism which he assured me it wasn't.

Well, looking at what he wrote about it again in his last debate post, I cannot help but again think that it is just a biased and anthropocentric view that intelligent design ended with mankind. In our private exchange, he assured me that there were good and valid scientific reasons for believing that intelligent design ended with humans, but he didn't provide any specifics there, nor (to my extreme disappointment) did he provide them here.

What I was looking for would have been something along the line of some specific biochemical structures humans have which would require (and thus be evidence of) intelligent design, which haven't been found in any other living thing since the time that H. sapiens appeared. In our private messages, he assured me there were some, but this would have been the time and place to present them and yet they just aren't here.

Given this, I not only don't see the compelling evidence that intelligent design exists at all in living systems, but I certainly don't see compelling evidence which says when it started or stopped occurring at any particular point in time or with the appearance of humans.

Lack of evidence seems to be a recurring theme here, and I wonder if we will continue to see more of it in posts to come...

Daniel "Theophage" Clark