DNAunion

DNAunion: Once again, that’s your personal opinion. And to arrive at that conclusion, you have to be reading stuff into the article that isn’t actually there.

DNAunion: You didn’t even read the article, did you? Behe was trying to get his class to critically examine – i.e., think about and question, instead of simply accepting at face value – evidences. After having them read both The Blind Watchmaker and Evolution:A Theory in Crisis – so that “both sides” views were represented - he presented the class with the Post article on whale evolution and asked them what they thought. Behe’s leading the class is immaterial (well, unless you are actually claiming something like…”Behe probably threatened to fail anyone who agreed with the Post article”, but that’s completely uncalled for and unsubstantiated).

DNAunion: Did whales evolve from Mesonychids? Or did they evolve from artiodactyls? Evidence points both ways (or at least did back in 1999). In 1990, the Post article claimed it was Mesonychids, and if some of the students doubted that, well, they seem to have been on the right track, ahead of schedule.

PS: Does anyone know if the matter of whale origins has been settled, and if so, for which possible ancestor?

[ December 07, 2002: Message edited by: DNAunion ]</p>

DNAunion

DNAunion: Won’t you concede, Nic, that Miller misrepresented several key aspects of Behe’s statements?

In case you want me to be more precise, I will be.

Won’t you concede, Nic, that Behe made it clear what the three required parts of the IC cilium were, and that Ken Miller quoted Behe’s statements on that, and that Miller did not raise any objection to Behe’s parts list, and that Miller did not offer any alternative parts lists, and then, when he claimed to have refuted Behe with his eel-sperm flagellum, that all three of the parts that Behe listed as being required were still present?

[ December 07, 2002: Message edited by: DNAunion ]</p>

DNAunion

DNAunion: Thought I’d spend some time checking out the other two links. Ken Miller didn’t disappoint me at all!

The one I won’t discuss is little more than a jumping off spot: a list of links to various other material. However, there was another of the three that was an actual article, and it too, like the other one I looked at, was full of distortions/misrepresentations/quoting violations.

Here’s the link:

<a href="http://www.millerandlevine.com/km/evol/design2/article.html" target="_blank">http://www.millerandlevine.com/km/evol/design2/article.html</a>

DNAunion: Once again, in a different article, Miller relies on quoting out of context and distortion.

Here is a fuller quote – note how the context dramatically changes the meaning of the partial sentence Miller lifted from Behe’s book.

DNAunion: Note that Behe explicitly states that it is a specific kind of evolutionary route that is completely incapable of producing an IC biochemical system: a direct route – one in which the system retains the same function throughout the process and with that function being performed by the same mechanism. That is context in which Behe said that a precursor system that is missing one of the required parts wouldn’t be functional – and he’s right. Take away any of the required parts of the IC core and an IC system cannot retain its function, nor could you approach it from the other end because without one of its parts, a to-be IC system could not perform its to-be function.

(Note also that Behe does not claim that it is impossible for ANY kind of evolutionary process to produce IC biochemical systems. In fact, Behe explicitly states multiple times that circuitous, indirect routes could produce IC biochemical systems. Behe’s claim of impossibility involves only a direct route, not all routes).

DNAunion: So the TTSS functions for cell motility by means of a paddling mechanism? Nope. Neither. Miller himself states later that the TTSS shows:

DNAunion: Let’s go back to the train of thought/material I just interrupted with that post from a later section…

DNAunion: No, what this means is that Ken Miller has once again misrepresented Behe’s position.

Behe himself, in his 1996 book, points out that parts of IC biochemical systems can perform other functions in cells. For example, when discussing the required components of the IC cilium (those three parts being microtubule “poles”, dynein “motors”, and nexin “linkers&#8221 , Behe points out…

DNAunion: Obviously, parts of an IC system having other useful functions in a cell does not necessitate that the system is not IC, despite what Ken Miller would have one believe.

DNAunion: Miller misrepresents Behe’s statement, though this time it is not entirely his fault. What Miller fails to realize is that Behe is still referring almost exclusively to IC biochemical systems, and when not to them, to “almost IC” biochemical systems: Behe has NOT broadened his statements to include all complex biochemical systems, despite what Ken Miller would have his readers believe. For example, look at how Behe started off the chapter from which Miller quoted.

DNAunion: Now, what did Behe discuss in chapters 3 through 7? In chapters 3 through 6 he discussed one irreducibly complex biochemical system per chapter.

Chapter 7 is a bit different – in it, Behe discusses a highly complex biochemical system that many would consider to by IC at first glance, since it is complex 13-step metabolic pathway involving 12 different enzymes, in which the numerous intermediates have no other function in the cell except as belonging to the chain leading to the final product (thus making it appear that the whole system is needed for a selectable function: part of a system leaves non-usable products), and whose final product is the only “purpose” the pathway serves, and with the final product being required from the start in order life to exist. Yet, despite all of this, Behe states that this system – the biosynthesis of AMP – is not IC.

Thus, when Behe, in chapter 8, refers back to the biochemical systems he discussed in the previous chapters he can’t actually use the term irreducibly complex, because although chapters 3 through 6 (actually, chapter 2 also) dealt with IC systems, one chapter didn’t. So by being technically correct, Behe has inadvertently confused things a bit.

What this means, basically, is that one should consider Behe’s statements in chapter 8 and thereafter as still being based upon IC systems specifically (since that is the main topic of the book) whenever doing so does not produce any contradictions or other problems: IC is the default interpretation and there has to be sufficient reason to conclude otherwise. And at no time should anyone consider Behe’s statements to be based on just any-old complex biochemical system.

Miller misses all of this and therefore misinterprets Behe’s statement to mean, literally, ANY complex biochemical system, AT ALL.

DNAunion: What a fine example of quoting out of context and distortion!

Here is again a lengthier quote than the words Miller lifted out of context.

DNAunion: Note that Behe states the blood-clotting system AFTER the fork is irreducibly complex: he doesn’t say that the whole blood-clotting system is. Yet Miller “refutes” Behe by showing that one of the proteins that plays its role BEFORE the fork can be removed and function still retained.

Miller’s mistake is indefensible because not only did Behe specifically name the point after the fork as the system that is IC, he also explicitly listed the components of the system: fibrinogen, prothrombin, Stuart factor, and proaccelerin. Note that the protein Miller says can be missing and function retained is NOT in that list.

DNAunion: Compound strawman.

First, the ID claim is not that each and every novelty of life was designed by an intelligence. That’s nothing more than an exaggerated distortion of an opponent’s position.

Second, ID doesn’t claim that the designing or instantiation of the design has to violate natural laws. A desktop computer contains systems that are IC: a computer will not form by natural laws alone: yet computers do exist, and without any of the laws of nature being violated. Intelligence directing a process can achieve things quickly and easily that spontaneous natural processes either can’t or won’t.

Finally, do we have any idea what might motivate Ken Miller to use underhanded tactics in an attempt to shoot down ID, instead of sticking to facts? Yes, we do. ID doesn’t fit his religious ideas.

[ December 07, 2002: Message edited by: DNAunion ]</p>

Nic Tamzek

Phew.

Well, in no particular order:

1) Thanks for the notes on IC core. I didn't think Behe had used the term, but I agree that it falls out quite readily once one is talking about required parts and unrequired parts.

2) Thanks for pointing out Behe's caveat about the fork on p. 86. I concede the point, Behe did explicitly exclude the stuff before the fork (most of the friggin' system, then) although if you read the description of the system on p. 84 or the diagram on p. 82 you would miss this. It is strange that I have not seen Behe point this out in rebuttal to Miller's argument, which he has used in several debates now I think.

Notably, a four-part system is rather less impressive than the whole thang, although the latter is what IDists usually focus on.

I would maintain however, that the fact that such things (as Hagemann factor) exist as proteins that are (a) important, though debatably "required" in humans, but (b) have been lost in other organisms gives us yet another data point supporting the "part is helpful, then eventually crucial" pathway to IC.

Hypothetically speaking, DNA, if a protein such as Hagemann factor were added to a simpler blood-clotting pathway, say to increase sensitivity of clotting response, and after a few million years of coevolution the clotting cascade became dependent on that new protein (such that if it were removed, clotting wouldn't occur), would this:

(a) Show that IC can evolve "directly" (Behe's usage)

(b) Show that IC can evolve "indirectly" (Behe's usage)

(c) Show that the system defined as "original pathway plus now required enzyme" wasn't IC after all.

That I have no idea what your answer will be shows just how ambiguous the IC def'n and argument remains in practice.

(Keep in mind that my example as proposed is hypothetical...a "what if")

A great many of us, Miller included I expect, prefer answer:

(d) It wouldn't matter much because any way you slice it, it is a point for the notion that the kinds of complex biochemical systems that Behe likes can evolve via natural processes.

Under view (d), the "it's not IC" argument and the "it's IC but it evolved anyway" argument are saying the same thing, just using IC def'ns (c) and (a-b), respectively.

(see links and refs on blood clotting evo, hagemann factor etc., here:

<a href="http://www.antievolution.org/cgi-bin/ikonboard/ikonboard.cgi?s=3df2d7d94ed1ffff;act=ST;f=9;t=3" target="_blank">http://www.antievolution.org/cgi-bin/ikonboard/ikonboard.cgi?s=3df2d7d94ed1ffff;act=ST;f=9;t=3</a>

...and note, DNA, that I made a note correcting myself and Miller regarding Behe's specification of the "IC core system" for blood-clotting.)


3) Another cool thing about Hagemann factor is that while the protein doesn't exist in whales, a pseudogene does, and guess what group the sequence is closest to?? That's right, artiodactyls!!

Unfortunately we have no mesonychid genes to sequence, so I can't help you with that. This is the clearest explanation that I've personally seen was at Thewissen's site, with alternative hypothesis phylogenetic trees showing the various possible interrelationships and arguing that the fossils supported a certain one with mesons. being more distant relatives but the link appears to not be working:

<a href="http://www.neoucom.edu/Depts/ANAT/Thewissen.html" target="_blank">http://www.neoucom.edu/Depts/ANAT/Thewissen.html</a>


4) We've been over the cilium before, and while it is clear that Behe identifies only the three components as required, it's also clear that he places a lot of emphasis on the "lots of proteins" and "really really complicated" as well, and the various simpler extant cilia show just how much diversity is possible to still have a functioning flagellum. So similarly to the blood clotting case above, Miller should make this clear as well.

However, as I've said before, Behe really should not have said (repeatedly) things like "the cilium is IC" and "blood clotting is IC" if what he *really* meant was "a small subset of cilial components is IC" and "a small subset of blood-clotting components is IC". The latter kinds of statements would have been much clearer but also much less impressive, and would have weakened the portion of the appeal of his book that depends upon the "gee, that's complex" sentiment.

While I'm talking about cilia, some minutae:

1) Denton (1986) was not as careful as Behe and did indeed explicitly say that the 9+2 flagellum was as simple as a cilium could get. The 3+0 ones must have come as a shock.

2) Evidently "nexin linkers" are still basically known only as blobs on electron micrographs, no one seems to have linked these blobs with a gene or protein sequence. This kind of lack-of-data problem is a powerful point for the "give it some time" counterargument to Behe.

Nic Tamzek

Regarding metabolic pathways, there is nothing in Behe's reply to Miller on lactose metabolism:

<a href="http://www.discovery.org/viewDB/index.php3?program=CRSC%20Responses&command=view&i d=441" target="_blank">http://www.discovery.org/viewDB/index.php3?program=CRSC%20Responses&command=view&i d=441</a>

...about using a new definition of IC for the lac operon. The "IC evolutionary pathways" detour was prompted by a different set of arguments, in response to a talk.origins FAQ (!) by Keith Robison on blood-clotting:

<a href="http://www.discovery.org/viewDB/index.php3?program=CRSC%20Responses&command=view&i d=442" target="_blank">http://www.discovery.org/viewDB/index.php3?program=CRSC%20Responses&command=view&i d=442</a>

Therefore the "metabolic pathways aren't IC" defense is nuked, because sometimes Behe treats them as IC, namely when he thinks it's a "winner" for him.

And anyhow, if it's accepted that natural evolution can produce the multiple-parts required Krebs Cycle, then why can't it produce other multiple-parts required systems like the flagellum?

My point about IC "really" only depending on "multiple-parts required" is that this characteristic is the only one that does any work in the Beheian argument. "Well-matched", "interacting", etc., are only invoked occasionally, almost always just to disqualify potential counterexamples. As the lac operon example shows, even Behe doesn't always consider these other criteria crucial.

nic

Nic Tamzek

Regarding multipart complexes in the TCA cycle, see here:

<a href="http://www.mednote.co.kr/BOKnote/tca.html" target="_blank">http://www.mednote.co.kr/BOKnote/tca.html</a>

...so at least there is an "IC core" of required, AND well-matched and interacting parts.

And yet peer-reviewed lit. exists on how it evolved, imagine that...

nic

Nic Tamzek

Regarding the supposed non-ICness of the TCA cycle, DNA writes,

Documentation if you get a chance...

So what? They're not performing the same function, so the presence of alternative uses does not disqualify ICness -- at least according to your argument about the flagellum:

So which is it, DNA -- do alternative functions for subsystems disqualify ICness of the whole, or not? If not, then the TCA cycle is still IC.


...but...but...ICness is not determined by evolvability, it's determined by multiple-required-parts and debatably a few additional things. Only if you define IC as "that which can't evolve 'directly'" does evolvability play a role in determining IC, but this turns IC into a tautology.

The way things should work is:

1) IC systems are clearly identifiable and identified based on a priori criteria

2) And then we test Behe's argument to see if there is evidence that they evolved via the common processes, e.g. NS of gene duplication/mutation etc.

...I didn't start it


Speaking of semantics, a question left for you:

Is hemoglobin IC or not, considering Behe's requirement that a "functional" system exhibit not just any weak function but at least a minimal function enabling the organism to survive?

DNAunion

DNAunion: Not to be rude, but to repeat something I said about a week ago, "Don't know, don't care".

I am not trying to defend Behe against all comers or against all potential counters; I'm no longer interested in every little nuance of Behe's position (it may seem like I am because my counters to Miller rely on details, but that is just stuff I happen to still remember and know where to find quickly). I am no longer in the "business" of fighting over ever little detail of any biochemical system someone wants to put forth as a counterexample to Behe's statements (or rather, people's personal (mis)interpretations of Behe's statements). I am basically interested in the errors I can spot from a mile off: such as most of the things I pointed out about Ken Miller's articles (some of the things are a bit iffy, but more of them are rock solid, in particular, the blood-clotting and cilia stuff). Again, let's not lose sight of the fact that I now fully accept undirected evolution as the mechanism behind common descent of all life forms. But I feel that gross misrepresentations of anyone's position should be pointed out: it's the right thing to do.

[ December 08, 2002: Message edited by: DNAunion ]</p>

DNAunion

DNAunion: I strongly disagree.

I first looked at the dates on the two papers to see when they were written – they both showed 07/21/2000. So we can’t tell which was actually written first. However, it is pretty clear that it took Behe more than just one day to compose these two articles combined, so it is pretty safe to bet that he was working on them both simultaneously. And under that safe assumption, regardless which one he completed first, he had the idea of the new evolutionary pathway definition of IC he mentions in the blood-clotting paper already well in mind and ready for use when he wrote the paper on the lac operon.

“That’s all well and good”, you say, “but can you provide us with anything that indicates Behe was using his new definition in the lac operon paper?”

Yes, I can do more than show that Behe’s use of the new definition in the lac operon would be consistent with the time of his composing that article. Here are some lengthy quotes.

First, from the blood-clotting paper, where Behe reveals his new definition for the first time (as far as we can tell).

DNAunion: Now look at the following from the article on the lac operon. I have highlighted some stuff.

DNAunion: In discussing the lac operon, Behe surely seems to be using his new IC evolutionary pathway definition, not his original 1996 IC biochemical system definition.

This is all the more clear since the lac operon does not meet Behe’s 1996 definition of an IC biochemical system, for more than one reason.

Synaesthesia

DNAunion,
Hm, I see he's openly embraced his absurd definition which rules out functional exadaptation.