Sunday, February 20, 2005

Something's fishy here...

In the responses to Serge’s post, Pharyngeal Phantasies?, over at Imago Dei, we see continued examples of how neo-Darwinists approach the idea of common descent in a circular fashion. If you recall, Serge raised the question, “if the structures of the human face evolved from gills in a fish, why are CN V and VII, derivatives of the first and second pharyngeal arches, not present in fish gills?” Serge was immediately taken to task for not only having too simplistic an understanding of the processes at hand, but for mistaking that we should expect evolution to operate in such a manner as to produce a one for one correlation between organisms which supposedly shared a common ancestor. Yet the arguments presented illustrate that the neo-Darwinists already assume that the evolutionary process has answered the question. Consider this scenario one dissenter presented:
The actual model is rather more like this: (a) start with a jawless fish with no jaws but lots of gill arches (b) the first few gill arches evolve into jaws (c) much later, this now-jawed lineage splits into teleost fish (most modern "fish") on the one hand, and tetrapods+lungfish and relatives on the other.
Keep in mind that the reason this is how the process is thought to have occurred is because of similarities in structure combined with a supposed functional advantage. This is how the process works – data is viewed through evolutionary spectacles and then unwarranted extrapolations are made. The key, for the neo-Darwinist, is not whether or not a process can be shown that produces common descent, but whether or not similarity in structure can be found. Thus, the gist of criticism such as Serge’s (and mine) is tossed aside under the pretense of nonsensical. One commenter to P.Z. Myers website even commented that my arguments never tell how anything occurred and, interestingly enough, that he found my arguments regarding “posts on how the bible doesn’t have moral relativism” to be “particuarlly [sic] funny” (one wonders what such an addendum has to do with cranial nerves - especially if all the neo-Darwinist is interested in are scientific explanations?). The problem with the reasoning going on by the neo-Darwinists is that they ignore the aspect of intentions – designer’s intentions. Should we assume that a lack of one for one correspondence between cranial nerves and pharyngeal arches is indicative of evolutionary processes, or should we assume that such a lack of correspondence indicates design? Consider the processes involved in engineering and construction projects. Although there are a variety of types of projects (e.g., refinery, power plant, highway, telecommunications) they typically involve using similar processes with which to achieve project completion. However, there are times when a particular phase of a project does not start even though it is physically possible to do so. In many government projects such an occurrence is usually due to the fact that the phase is not only dependent on its physical predecessor, but on legislated monetary funding as well. Government projects have the idiosyncrasy of having additional pathways, through which activities must flow, in order to achieve project completion. That such red tape stricken processes may be inefficient is beside the point, for what must be understood is that despite it appearing that a designer would not have chosen such a pathway, it is an intelligently designed pathway nonetheless. Another example would be that of a software system designed to produce monthly data for a company with regards to the status of a particular project’s financial status. Suppose that we find out that the same type of monthly data for two different projects is produced by different software code pathways. What gives? Would we be justified in concluding, because the two different pathways produced similar type of data, that the pathways were not intelligently designed? Certainly not. And not simply because we happen to know that the software was intelligently designed. The error in such a conclusion is due to the fact that the outside observer is simply not aware of why the different pathways were used. It just so happens that the type of contract the project was brokered under will determine the manner in which the financial data is calculated. This key factor indicates why two dissimilar pathways are used to achieve similar outcomes. Without understanding the full parameters of the process, as well as the intentions of the designers, claims that the system was not designed are unwarranted. That similar structures can be purposely designed to produce various functions, and that various structures can be purposely designed to produce similar functions, indicates that the designer's intentions must be considered when analyzing how functional systems came to be. And intentions can only come about through a mind. --- For further reference, check several posts I wrote regarding how planning and scheduling relates to the concept of intelligent design. I didn't Plan it that way... What are your intentions?... Attributes of the Designer... A Scheduling Nightmare... ---- Update: check Unintelligent Design, at the NYT, for another example of unwarranted assumptions. HT: World


RA said...

I have found most evolutionists, when confronted with embarrassing science, attack the individual instead of trying to refute the arguement. This tactic works with the young and the ignorant. But with thoughtful people it shows they have no answers for the thousands of gapping holes in evolutionary theory. Often I am asked to prove ID as a way out of answering my embarrassing question. Since evolution nor ID can be proved it is nothing more than a stall. The best we can do is see wether the science we know today substantiates or denies the possibility of either postuale. Overwhelmingly, evidence we have today says evolution could not have happened. Can you be 100% sure? No, but the evidence we do have says it was impossible. The only reasonable alternative is ID.

LotharBot said...

Myers' arguments on his site are rather unfortunately framed -- reading half a dozen of his most recent entries shows he's far more interested in flamewars and insults than he should be (see: here.) That doesn't tend to lead to good discussion with the people he's arguing with. No matter how ill-informed they might be (and, having read a few comments, some of them *are* ill-informed), the name-calling that goes on there is not conducive to learning. That's too bad, because he probably has quite a few things to contribute to the discussion... as ra said, this particular evolutionist has resorted to attacking the individual (though I disagree with the assertion that he's typical -- I know quite a few evolutionists who don't descend to such depths.)

As I mentioned in the comments to a previous post, homology is really poor evidence for evolution. It's best treated as an inspiration for theory -- we see similar structures, so we hypothesize that there might be some correspondance, and then we look at DNA sequences and gene expressions and such to figure out what's really going on. It's similarity of DNA, not similarity of external structures, that should be used to analyze possible evolutionary pathways between creatures. (Though, in some cases, the homology is strong enough that looking at the DNA is something of a formality.) Myers posted a response to the Imago Dei argument that does look more at the genetic level, and that's where the argument should really focus.

ra, I'd be curious to see the "evidence" we have that says evolution could not have happened. I used to think such things existed when I was a high-school freshman who thought websites with "creation" in their names were unbiased, but I know better than that now. Almost every argument I heard at a younger age about how evolution was "impossible" badly mischaracterized evolution, to the point where nobody who actually knows what evolutionary theory says would take the arguments seriously (and they'd be completely justified not to.)

Finally, let me repeat: ID is not an "alternative" to evolution. ID is an alternative to philosophical naturalism. Evolution is compatible with either framework. There are still ways in which it needs to be tested, and there are still gaps in the theory, but evolution can fit with either naturalistic or intelligent causes...

Rusty said...

Yes, I’ve pretty much given up attempting dialogue with him.

I believe that God is capable of using the process of evolution as described by neo-Darwinists. But I also believe that the physical and Biblical evidence indicates he did not.

What are your thoughts of the recent National Geographic article Was Darwin Wrong? It seemed to me that they relied heavily on the concept of homology as a basis for concluding that evolution was valid. Regardless of the level of where the argument should focus, and I do agree that the DNA level will pretty much seal the debate, one should continue to be aware that similarity of sequence in structure and time does not necessarily give credence to the idea of common descent. The similarities could just as easily be explained by the ideas of templates and planning. Whether or not these ID concepts can be tested does not diminish whether or not they are true. I know that will not sit well with those who require testability, but the issue I’m addressing is truth… if the concept of ID cannot be confirmed (yet) by testability, then it cannot be excluded either. While it may not be “science” it may still very well be true.

LotharBot said...

"I ...believe that the physical and Biblical evidence indicates [God] did not [use neo-Darwinian processes]."The short version of my thoughts:

1) The Bible doesn't really address the issue. Genesis 1 is not intended to be a cosmology, it's meant to contrast God with the myths and idols the Israelites were familiar with. God creates intentionally (others created by accident); God is sovereign (others were subject to nature); God rules over ALL creation (others made or controlled only parts of it). For further reading, see my wife's post on hermeneutics and her EXCELLENT post on Genesis 1.

2) The physical evidence is still being evaluated. Parts of the process have been tested and evaluated and pretty much nobody argues about them any more, and other parts still need to be dealt with. Overall, the neo-Darwinian paradigm works very well on a short-term small scale in the lab. When we look at things on a larger scale, like DNA similarities or homologies of fossils, we get results that are at least marginally compatible with the current state of the theory. There isn't anything blatantly *broken* about the current theory, at least not anything anybody (evolutionist or not) is aware of. There are just gaps -- speciation and cladogenesis haven't been studied deeply enough, for example. The only thing I can really say at this point is that I'm still evaluating the evidence, and I think everyone else should be too.

"What are your thoughts of the recent National Geographic article Was Darwin Wrong? It seemed to me that they relied heavily on the concept of homology..."I glanced over it. It was all pop science -- exactly the sort of stuff I've consistantly criticized. Homology is simply not very good evidence for evolution, and the article was basically all homology (and not even very cutting-edge, if I recall correctly.) The article was apologetics, not science.

"one should continue to be aware that similarity of sequence in structure and time does not necessarily give credence to the idea of common descent [instead] of templates and planning."If I may hijack some terminology for a moment:

What we're looking for in DNA is not merely similarity, but "specified" similarity. That is, we're not just looking at some vague measure of "this sequence kinda matches the other sequence", but rather, looking at the ways in which they differ and the ways in which they're similar. How do the actual sequences compare to what a pure template system would give, vs. what a pure mutation/selection/drift system would give?

In a pure template system, one might expect DNA to differ only in those areas where the differences are significant. That is, one might expect the minimum number of changes, and no "useless" changes. As you've said before, you would not expect junk DNA. But, more than that, you would not expect "worthless" mutations.

Now, if you look at actual DNA sequences, it's very common to find tons of "worthless" mutations. By "worthless", I mean, DNA mutations that don't change the protein structure at all. If you look at a list of codons you'll notice there are a lot of ways to code for the same thing (for example, CG_ codes for Arg no matter what you put in the _.) When looking at different species' DNA, we tend to see a lot of variation in these trivial ways, which I doubt we'd see so much of in a pure template system. On the other hand, such variation fits very well with the neo-Darwinian formulation -- of course you see mutation there; such mutations are neutral, so they're expected to occur and stick around.

In general, we can analyze different DNA sequences and look at how they differ in terms of:
- mutations in the third position of codons vs. first/second
- insertions, deletions, and changes in coding regions of different types (genes, regulatory segments, etc.)
- duplication or partial duplication of segments of DNA (especially where the duplicate segment is broken up in such a way as to be useless.)
There's a lot more, but I left the textbook that describes these in detail in my desk at school.

I'm not saying this proves things one way or another... but it does demonstrate that if the DNA evidence is analyzed carefully enough, it may give a lot more credence to one theory than another. I used to really like the "template" theory, but I'm not so sure it's all that good, having looked at the level of mutation we're actually dealing with between species.

"if the concept of ID cannot be confirmed (yet) by testability, then it cannot be excluded either."Of course not. All anybody can really say is "come back to me when you've got a working theory." Right now, trying to apply ID to origins is just a waste of time. Once the theory has been developed on easier problems, it may be able to be made robust enough to try to apply to biology.

LotharBot said...

By the way: Chicago Boyz has a very interesting discussion about the inflammatory rhetoric that both Christian fundamentalists and Secular fundamentalists tend to use.

Rusty said...


I would argue that the creation account in Genesis 1 (and there are other references in the Bible to creation) was primarily intended to explain that God created the natural realm, is separate from it, and is sovereign over His creation. This contrasted, as you allude, with virtually every other creation account of the day and, especially, with the Egyptian religious structure. It's interesting that we also see this contrast in the account of the 10 plagues brought upon Egypt. Far from being random in nature, the plagues were a systematic tearing down of the religious system that the Egyptians followed.

Another intent, I believe, was that the creation account in Genesis 1 gave us the workday/Sabbath (6/1) pattern that was the foundation for many of the OT laws to follow.

Of course we can inductively draw many more truths from the creation account, and the first few chapters of Genesis, but those two should be pretty clear.

Now while the creation accounts in the Bible are not intended to be scientific portrayals, at least two important points should be highlighted: 1) the text should not contradict what we know about the physical world and, 2) what we know about the physical world should not contradict the meaning of the text.

The burden is then on the one who posits that natural forces can evolve a new species to harmonize such an idea with the meaning of the Hebrew words that reference the action as being only by God's direct interaction. (note: I realize I've greatly simplified the issue with that statement... but I think my point should be understood) Similarly, the burden is on one who posits that the six days of creation were 24 hour periods to harmonize that idea with the evidence that points to a universe 13.7 billion years old.

A very quick way to say that I think the Biblical evidence (not just Genesis 1) indicates that the evolutionary process, as posited by neo-Darwinism, is not how God performed his creative work. Yet I also think that the Biblical evidence allows for a universe that is billions of years old. Note that I am not saying that God couldn't have done it one way or the other. BTW, I couldn't access the links to your wife's commentaries.

I would agree with you that things in the lab on a short term scale probably work. I've never disputed that (although I've heard arguments that such experiments are sometimes helped along by researchers). My beef is with the extrapolations that are made - evolutionists consider them justified, and I disagree.

I don't have to tell you that genetic sequencing is incredibly complex. Michael Denton describes what I term "integrated complexity" in which changes to one part of a system affect another part, all unbeknownst to the scientist. You see it happen all the time in software programming - one change, meant to fix a bug, raises another unexpected issue. So, I would argue that before one can justify a claim that complex sequences are "worthless," one must first know more about the system and how it functions as an integrated whole. In the engineering world, if the intentions of the designer can't be discovered, then all we're left with is finding out as much about the system and its function(s) as possible. I see no difference in the genetic world.

When you say "origins" are you meaning the origin of species or the origin of life? You might want to reference Rana & Ross' book Origins of Life sometime.

PZ Myers said...

Tsk, tsk. Read the criticisms again.

The objections are that Serge made an embarrassingly bad mistake in assigning homologies: the tetrapod jaw is not homologous to the teleost first gill arch. Fish have perfectly good jaws, you know.

What's really fishy is the way creationists persist in their delusions. Is it intentional, or are you really incapable of comprehending the biology?

Rusty said...


First off, thanks for responding in a more civil manner. I do appreciate it.

I'll be the first to admit that my arguments do not address the details of the science at hand. Not being a scientist, it would be foolhardy of me to attempt such a dialogue. What I do attempt to illustrate is whether or not arguments posited by neo-Darwinists are based on faulty thinking. Hence, I addressed a couple of examples of such in my post.

LotharBot said...

On Biblical InterpretationRusty, it's possible the comments my wife made were inaccessable recently. The board she posted them on has undergone a couple of DoS attacks recently (and the admins may be requiring registration to read; I don't know.) Try again; they're good posts, though it sounds like you've got the main points of them already. I agree with most of what you said about Genesis 1 up until the end of your post.

Rusty said: "The burden is then on the one who posits [X] to harmonize with [Y]"Well... the burden of proof is always on whoever posits anything, when trying to convince others in a debate context. But, responsible scholarship on our part means that we'll evaluate what others say, whether or not they have actual proof, and whether or not their motives are trustworthy. Typically, "the burden of proof is on you" is a cop-out response. Real scholars will do their best to evaluate evidence, even if it hasn't been proven, and even if it's coming from people whose motives are questionable. And Real Scholars will recognize uncertainty, withhold judgement, and be comfortable with the fact that they don't really know.

Rusty said: "I think the Biblical evidence [indicates evolution] is not how God performed his creative work"We'll have to have this discussion sometime, then. I don't think the Biblical evidence indicates much of anything at all about the process.

On ID and evolutionary theoryRusty said: "My beef is with the extrapolations that are made..."Agreed... sometimes. This is why we need better models and better experiments. It's far too big a question to be left to extrapolation on the short-term, and the only truly long-term experiment I'm aware of (with corn over 100 years) involves strong artificial selection, and isn't all that remarkable.

Rusty wrote: "When you say "origins" are you meaning the origin of species or the origin of life?"In response to my statement: "trying to apply ID to origins is just a waste of time"I was thinking specifically of species here; I asked a related question in another post about the nature of the universe. Either meaning would fit the general sentiment, though -- ID isn't ready to be used on problems that complex yet. New scientific or mathematical methods need to be developed and tested on toy problems. If you come up with a new method, the absolute first thing to do is try it out on an example you know *everything* about and see if your method gives you true answers. Then you try it on slightly harder examples, develop stronger understanding of how your method performs, and revise your methods to work better. ID, right now, hasn't gone through a sufficient "toy problems" stage to be a useful science. It's intuitively compelling, but it needs a lot of work, and unfortunately its main proponents are busy trying to use it on problems it's not ready for.

Trying to apply ID to origins with the ID tools we have now would be like trying to apply mathematics to fluid dynamics pre-Newton. You can do a little bit using just algebra, but you really need PDE's to deal with fluids. The mathematical tools pre-Newton weren't ready to deal with fluids, and the ID tools right now aren't ready to deal with much of anything.

On civil discoursePZ Myers wrote: "...creationists persist in their delusions... are you really incapable of comprehending the biology?"Rusty, I don't think he was being more civil here (unless that was a generic "you" rather than a specific "you".) I think he was trying to call you a deluded creationist, and brush you off. Like I said, he seems far too interested in flames and insults...

Some people from opposing viewpoints will help you understand where they're coming from, teaching you and guiding you and respectfully answering your questions, and they'll try to understand you at the same time. This is how my wife and I have answered atheists for years over at the DBB, and it's no surprise that almost all of them respect us and most have become much more friendly to Christianity. Others from opposing viewpoints will call you names and throw facts or assertions at you, which might help you understand that single point a little better, but will not particularly endear you to their position. PZ, I encourage you to consider changing tactics for the sake of civil discourse, in spite of whatever ill will you have toward whatever class of people you percieve Rusty as belonging to.