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