Found this via Pharyngula:

Mirecki hospitalized after beating

Douglas County sheriff’s deputies are investigating the reported beating of a Kansas University professor who gained recent notoriety for his Internet tirades against Christian fundamentalists.

Kansas University religious studies professor Paul Mirecki reported he was beaten by two men about 6:40 a.m. today on a roadside in rural Douglas County. In a series of interviews late this afternoon, Mirecki said the men who beat him were making references to the controversy that has propelled him into the headlines in recent weeks.

...

Mirecki recently wrote online that he planned to teach intelligent design as mythology in an upcoming course. He wrote it would be a “nice slap� in the “big fat face� of fundamentalists.

The remarks caused an uproar, Mirecki apologized, and KU announced last week the class would be canceled.

Here’s PZ Myers new definition of fundamentalists:  ignorant thugs with a Bible.

It’s no surprise, sadly—I’ve long known that Christian fundamentalists/conservatives are hateful, violent goons. And I’ve got quite a few friends at KU, too. Perhaps I should tell them to hire bodyguards.

As a prominent member of the Society of Open Minded Atheists & Agnostics (SOMA) group here on campus that has been assosciated with this witch hunt, I can say that I don’t intend to leave my room without some form of weapon.
And I should say I’m not surprised by this story in the least. If people don’t think “good christians” would do crap like this, perhaps you should look up the story of Joann Bell, who’s children were attacked and her house burned to the ground while the local fire department refused to put it out.

Are you a KU student, VR?

If people don’t think “good christians� would do crap like this, perhaps you should look up the story of Joann Bell, who’s children were attacked and her house burned to the ground while the local fire department refused to put it out.

Arson is such a Christian act, isn’t it? (actually, any more it is)

Are you a KU student, VR?

Yes I am. I’m a junior working on a dual major in physics and astronomy. I joined SOMA shortly after the semester started and have been one of the most active members since then. Dr. Mirecki is a good friend of mine and this disgusts me greatly.

Were it an isolated incident, I might brush it off, but this is actually fairly common and it’s hit close to home. I’m considering switching schools thanks to this event.

Cool. I was originally from Wichita, and if you think the climate in Lawrence is currently scary, I wouldn’t advise going to the Air Capital anytime soon.

Cool. I was originally from Wichita, and if you think the climate in Lawrence is currently scary, I wouldn’t advise going to the Air Capital anytime soon.

Again, I don’t intend to leave my room unless absolutely necessary (ie, class and food) and when I do, I’ll be carring some sort of self defense.

Warbi, thanks for pointing out the fact that Behe’s “replies� are seriously outdated versus the newer studies. It makes you wonder of Myxi is even bothering to read what we’ve presented seeing as he appears to think he has rebutted it already.

Well, let’s check it out.  One link went to a book review of Behe’s book by Kenneth Miller, dated 1999.  So this one fails the “outdated” accusation by two years in comparison to the Behe site.
Another link was provided by Nowiser which led to American Scientist, September/October 1997, another review of Behe’s book.  In comparison to the 2001 date of Behe’s site, this one fails by four years. 
Nowiser also provided another link which he said would lead to 70 other links critiquing Behe’s work.  He claimed: 
[if you scroll down on this page, you get about seventy links that address flaws in Behe’s work, from the general to the very specific, from IC to the blood clotting cascade in vertebrates.]
But not all of the links were critiques of Behe’s work.  In fact, some of them were links to articles written by Behe, and many of them were actually Intelligent Design articles.  Most of the links, though, were from 1997-1999, there was only one I found that was later, from May 2000—which is still two months before the date of July 2000 on Behe’s article detailing what was wrong with the supposed “rebuttals” of his work.  He dealt most specifically with Miller’s Finding Darwin’s Box. 
And the fact is, it was Miller’s study which I referred to when I said Behe had already blown his findings out of the water.
This one fails, for the most part, by 2-4 years on all links, but hey, you’re getting warmer—there at least was one link from the same year as Behe’s article critiquing Miller—though it still was published two months earlier. 
From what I can tell from scrolling the thread once again, that leaves only one other link that was posted to which I have not responded.

Just wanted to point out that all of Behe’s rebuttals <--- linked by Mxyzptlk earlier take us only to essays and interviews he (Behe) has written which date to no later than August 2001. In other words, anything anyone in the scientific community has written in the last four years about his ideas has not been responded to at this link. Like, for example, the 2003 article Les pointed us to which debunks Behe’s flagellum irreducibility nonsense.

I can’t believe you’d actually go there again, but hey, I’m game.  Les has already accused me of “dismissing outright” the pages linked to.  I don’t feel that I have.  But in this particular case, if I had done so, it would have been well-deserved.  The fact is, it is not a rebuttal, it is a proposal for a model to be tested.  It at least has one feature going for it that the other links do not, it cites from works after 2001.  But the nature of those citations from newer sources are very benign, dealing with general information about the flagellum rather than with the flagellum’s evolution.  The statements generally read, “Scientist X has observed feature Y on this flagellum.”  The latest source which was not of that nature was one that the study seemed to return to, more than once.  But it was stated concerning this study from 2000:

Although Rizzotti does make use of some interesting similarities between the flagellum and ATP synthetase, and he is able to come up with a proposal that includes rotary motion from the beginning, there are major flaws which shall be discussed shortly.

So the most significant study from which this particular model draws support has “major flaws.”  But check out what else is said:

As Rizzotti’s scenario fails on the twin tests of homology and a simple model of stirring at a low Reynolds number, it is now time to see if Rizzotti can be improved upon. It should be noted that although published proposals about flagellar evolution are very limited, the topic is a popular one as the flagellum is the icon of the antievolutionary “Intelligent Design� movement. Therefore several of the ideas proposed here have been previously raised in informal debates about flagellar evolution. Miller (2003, 2004) and Musgrave (2004) review this aspect of the debate in detail, and Musgrave proposes a model that is similar in outline to that presented here, although his account is more general.

So this study is being done to address what has become a “popular topic” because of ID arguments.  In other words, there was an agenda before they even began, to try their best to find something to counter these damn “antievolutionists!” Gee, I wonder what the results will be when this model is submitted to testing?  But let’s see how they summarize what their expectations are of the model proposed:

Of the 30 major structural components listed in Table 1, 12 are axial proteins and probably share a common (unidentified) ancestor, a hypothetical type III pilin subunit. Of the remaining 18 components, four (FliI, MotA, MotB, and FliM) have well-accepted nonflagellar homologs based on significant sequence similarity. Suggestive evidence of homology exists for eight components, FliHJOPQR (with components of the ATP synthetase), the P-ring FlgI (with secretins), and the lipoprotein FlgH (with lipoprotein chaperones of secretins). On the basis of interactions with other components with identified nonflagellar homologs, homologies can be postulated, with little current supporting evidence, for two components, FlgA (with other secretin-associated proteins secreted by the type II secretion system), and FliG (with a fragment of a TolA homolog). Finally, five components (FliF, FlhA, FlhB, FliN, and the ancestor of the axial proteins) have no identified potential homologs, although nonflagellar ancestral functions are not difficult to postulate. The type III virulence system contains homologs of most of these proteins (probably including an axial protein; Cordes et al., 2003), but as discussed previously its phylogenetic position is controversial. At this early stage of investigation this mixed bag should not be surprising. Structural information (which is conserved even when sequence similarity is lost) is not available for most of the proteins, and current sampling of bacterial genomes is not very balanced. However, the homologies postulated provide opportunities to test the model with future observations: if the model presented here is correct, then it is expected that nonflagellar homologs for most flagellar proteins will be found serving the suggested functions, in the suggested systems. Similarly, the model can be falsified by discovery of homologies in unexpected locations: for example, if the proteins of the flagellar basal body are discovered to be homologous to proteins of the junctional pore of gliding motility rather than a primitive type III secretion system, then the entire model would be overthrown and replaced by a model relating these two systems.

A “mixed bag,” unavailable “structural information,” “not very balanced?”  How exactly does this refute anything Behe has said?  That is, how does an untested model, based primarily on a study with “major flaws,” and with other admitted problem areas, somehow come across to you as a “rebuttal?” Failed again.

Voija:

You said earlier that a mole was responsible for leaking the e-mail.  From the SOMA forum:

The reason Kansas knows about the email is that Dr. Mirecki, who lost his common sense on the way to becoming a Professor, posted it on a publicly accessible forum.

http://pub13.bravenet.com/forum/1083743891/show/500229
See Ray Pence, 2nd Post.

All one had to do to read what the guy wrote was register.  Your chapter president confirmed that as well.  It seems that you have exhibited the capacity in the past to dramatize the sitation.  Accordingly, I shall view your most recent comments in light of that. 

Elwed:

I’m going to reserve judgment about the motivation of the attackers until the investigation is complete.  Seen too many Tawna Brawleys to jump the gun.

I do note that the story talks about contact to the upper body that results in some bruising and soreness but no mention of stitches, no broken nose, no split lip, no facial lacerations. WTF? These attackers punched him in the shoulder and/or chest? Also, the attacker was wearing women’s golf wear?  I can’t wait to see wait to see the mug shot for this guy.

I’m sure he should be arrested by now anyway. A college professor surely got the plate from the attacker’s vehicle that had to either go past him as it left the scene or turn around from its parked position immediately behind the professor’s vehicle, and towards which the professor walked, before it could drive away. Turning around, depending upon on how the turn was initiated, would in almost all instances bring the car even closer to the professor and would expose the required back plate. So, more will be revealed.  I may be doing a mea culpa on here for this portion of this post, but time will tell.

Consigliere, I never said that the forum wasn’t accessible. However, these is to be a distinct line made between “accessible” and “public”. Again, this listserve was explicitly labeled as a SOMA group and anyone entering should expect to find things with which they’d take exception.

John Altevogt, the one that leaked the Emails, joined with the express intent of finding something to publicize in order to discredit Dr. Mirecki. Furthermore, if you look at the history of SOMA’s emails you’ll find that comments such as Dr. Mirecki’s are rare although not unheard of. However they are clearly tongue in cheek and were quoted severaly and malicioiusly out of context.

In regards to the attack, I’m not sure which sources you’re looking at, but Dr. Mirecki suffered a concussion and a broken tooth as well from the attack. I’m not sure where you got the “women’s golf wear” comment from. Does “red visor and wool gloves” = “golf wear”?

Additionally, Dr. Mirecki did not get a plate number. He recounts blacking out at some point and waking up after the attackers left.

As the fish sitting in the teapot in The Cat in the Hat Comes Back said, “Do I like this? Not one little bit!”  But here I am again…

Myxi, it’s obvious you don’t want to leave the merry-go-round of “well, my source says” and now “well, my source is more recent than yours”.  You have yet to demonstrate any understanding of the subject.

A good example of this: you quote Matzke’s proposed model of the evolution of the flagellum...

Although Rizzotti does make use of some interesting similarities between the flagellum and ATP synthetase, and he is able to come up with a proposal that includes rotary motion from the beginning, there are major flaws which shall be discussed shortly.

...to which you say

So the most significant study from which this particular model draws support has “major flaws.�

Myxi, you obviously did not read Matzke’s paper, but just scanned it for quote mines- or perhaps you just read some ID’er who scanned it for quote mines.  If you had actually read it, as I did, you would have noticed that Matzke’s discussion of Rizotti’s model came under the heading of “Previous attempts to explain flagellar origins”, and that Matzke’s model draws no support from Rizotti’s.  So Myxi- either you did not understand Matzke, or you did and are being disingenuous.  In either case, why should we listen to anything you say about this?

You close by quoting from Matzke’s evaluation of his proposed model, where he addresses its uncertainties and weaknesses, and you comment

A “mixed bag,� unavailable “structural information,� “not very balanced?�
How exactly does this refute anything Behe has said?  That is, how does an untested model, based primarily on a study with “major flaws,â€? and with other admitted problem areas, somehow come across to you as a “rebuttal?â€?
Failed again.

No, you just didn’t understand what’s going on here.  The study with “major flaws” I’ve dealt with above.  The pointing out of imperfections in understanding does not demolish a scientific model- something can be plausible even if it is imperfectly understood, if the evidence for it is coherent and sufficient- admittedly, not always easy to decide.

But the main problem here is that you obviously think it takes a complete, corroborated description of the evolution of the flagellum to disprove Behe.  Not so.  Of course, a plausible model of how it could have happened, which is all Matzke is proposing, tends to cast doubt on Behe’s claim that the flagellum could not have evolved.

But what exactly is Behe’s, and ID’s, claim?  That the flagellum is irreducibly complex- that is, that every single part of it is necessary for function, and that no part is useful without the others (otherwise they could have evolved separately, and the whole structure is thus not irreducible).  It is this which has been disproven, as pointed out by Matzke:

The existence of a nonflagellar type III export apparatus falsifies the argument that flagellar components are useless if they are not part of a fully functioning flagellum. One answer to Macnab’s (1978) query, “What advantage could derive…from a ‘preflagellum’ (meaning a subset of its components)� is now obvious: a subset of flagellar components could serve as an export system.

The proteins of the export apparatus referred to, which is also known as the Type III secretory system or TTSS, are directly homologous to the proteins forming the base of the flagellum.  The TTSS has an important function- to make some bacteria nasty.  As Ken Miller (2003) puts it

Stated directly, the TTSS does its dirty work using a handful of proteins from the base of the flagellum. From the evolutionary point of view, this relationship is hardly surprising. In fact, it’s to be expected that the opportunism of evolutionary processes would mix and match proteins to produce new and novel functions. According to the doctrine of irreducible complexity, however, this should not be possible. If the flagellum is indeed irreducibly complex, then removing just one part, let alone 10 or 15, should render what remains “by definition nonfunctional.” Yet the TTSS is indeed fully-functional, even though it is missing most of the parts of the flagellum. The TTSS may be bad news for us, but for the bacteria that possess it, it is a truly valuable biochemical machine.

Irreducibly complex?  Not hardly.  Myxi, if you want to debate science, it’s not enough to wave around quotes from authorities.  You have to research and understand the subject.  The appeal to authority works in religion, but not in science.

One last comment.  You say

So this study is being done to address what has become a “popular topicâ€? because of ID arguments.  In other words, there was an agenda before they even began, to try their best to find something to counter these damn “antievolutionists!â€?

Most scientists, and rational people of all stripes, couldn’t care less what IDers believe, any more than we care about flying saucer abductions or golden hemmorhoids.  The problem is that the “damn antievolutionists” have their own agenda- to insert their religious views into public school science classes.  That is what bunches up our panties, and gives us our own agenda: to fight this attempt to force religiously motivated bad science on our kids.

Myxi, it’s obvious you don’t want to leave the merry-go-round of “well, my source says� and now “well, my source is more recent than yours�. You have yet to demonstrate any understanding of the subject.

I didn’t start that merry-go-round, I just jumped on—and if you look at the posts, you’ll see quite a few others had already jumped on before I got there.  Where’s your criticism of them?  Oh, that’s right, I forgot, those are the ones that agree with you.

Myxi, you obviously did not read Matzke’s paper, but just scanned it for quote mines- or perhaps you just read some ID’er who scanned it for quote mines.

Why the disparaging assumptions?  Did you arrive at these by scientic method?  Once again, I remind you I am not the topic here.  No, I read the entire article and reported on what it clearly had to say.  If you have a problem with quotes, then I suppose you should never quote?  Me, I quote for support so you can’t make the accusation that it’s my own opinion. 

In either case, why should we listen to anything you say about this?

I’ll say this again, since it appears necessary once again:  I am not the subject.  You don’t have to believe me, just read the piece and see the conclusions.  If I missed that point, it still does not change the conclusions. 

If you had actually read it, as I did, you would have noticed that Matzke’s discussion of Rizotti’s model came under the heading of “Previous attempts to explain flagellar origins�, and that Matzke’s model draws no support from Rizotti’s.

That’s a strange estimation of what was said.  If he drew nothing from Rizotti’s earlier work, then why would he introduce his concluding paragraph on Rizzotti (and actually on that entire section) with,

it is now time to see if Rizzotti can be improved upon.  “Improved upon” implies building upon the foundation Rizzotti supplied, while tweaking it for the flaws he sees in it.

The puzzling thing is that you would attempt to suggest that “previous attempts to explain flagellar origins” should be taken to mean that everything he says under the heading gets discarded or is worthy of no merit or consideration, or whatever it is you seek to imply.  Any researcher worth his salt will ALWAYS take into account the work that has been done in the field before him.  He mentions several, but when he comes to Rizzotti’s, he says:

The only major recent attempt at explaining the origin of the flagellum is that of Rizzotti (2000)

That clearly says his view of Rizzotti’s work is that it is the primary work among the few that have been done in this very specific field.  He further illustrates his high estimation of it by discussing Rizzotti at length.  If you read the entire section on “previous attempts,” it is easy to see it is in ascending order:  “short discussions,” “Cavalier-Smith,” and “Rizzotti.”  He spends more time on Rizzotti than on the other two combined, he calls it the “only major recent work” on the subject, and describes his own effort as an attempt to see if he can “improve on it.”  And when he gets ready to move on from “previous work” to the main part of his presentation, he doesn’t say, “Now let’s see if we can improve on all these scientists’ work,” he says, “Let’s see if we can improve on Rizzotti. 
Apparently you’ve got your mind more on me than you do on my comments.  You may go the route others have chosen here if you wish, and continue to engage in ad hominem remarks that attempt to make me the subject.  But you would be better served to simply stick with the material rather than accuse me of not reading the material.  You may ridicule me as not understanding science also, that does not faze me in the least.  I never claimed to be a scientist, and I am not in my field in a science discussion.  But I saw no requirement when I registered implying it was necessary to hold a science degree before joining in here.  And it doesn’t take a rocket scientist to read this report and see what is being said and what is not.  It’s there in plain English, and that’s one place where I am in my own field, particularly in observing how someone structures an argument. 
Why not simply stick with the material as presented, and make your case from it instead of character assassination?  For instance, I said Matzke used a report from Rizzotti that had “major flaws” in it.  A good counter would certainly have been, “But Matzke articulates the errors, highlights the strengths, and then says he intends to “improve upon” Rizzotti’s model.  Therefore, Matzke clearly indicates he is discarding the errors, that negates any accusation he is adopting the report, errors and all.”  (Or as we used to call it, “chewing up the meat and spitting out the bones.”)
The most extensive quotes I posted were his own estimation of the model.  (If you wish to challenge this, it should be easy to refute—it was included in the section titled “Conclusions.”)  So you wish to address it as though it’s pretty solid stuff?  Let’s look at it again:

4.1. Evaluating the model
Biological evidence supporting the model is summarized in Table 6, in terms of extant analogs to the hypothesized intermediates and nonflagellar homologs of system components. Of the 30 major structural components listed in Table 1, 12 are axial proteins and probably share a common (unidentified) ancestor, a hypothetical type III pilin subunit. Of the remaining 18 components, four (FliI, MotA, MotB, and FliM) have well-accepted nonflagellar homologs based on significant sequence similarity. Suggestive evidence of homology exists for eight components, FliHJOPQR (with components of the ATP synthetase), the P-ring FlgI (with secretins), and the lipoprotein FlgH (with lipoprotein chaperones of secretins). On the basis of interactions with other components with identified nonflagellar homologs, homologies can be postulated, with little current supporting evidence, for two components, FlgA (with other secretin-associated proteins secreted by the type II secretion system), and FliG (with a fragment of a TolA homolog). Finally, five components (FliF, FlhA, FlhB, FliN, and the ancestor of the axial proteins) have no identified potential homologs, although nonflagellar ancestral functions are not difficult to postulate. The type III virulence system contains homologs of most of these proteins (probably including an axial protein; Cordes et al., 2003), but as discussed previously its phylogenetic position is controversial.

(1) 30 major structural components are evaluated
(2) only 12 are accepted straight out
(3) 4 have “significant sequence similarity
(4) 8 have “suggestive evidence”
(5) 2 have “little supporting evidence”
(6) 5 have “no identified potential homologs.

Again, no rocket science here.  The evaluation is in descending order of the findings.  He was right to refer to it as a “mixed bag.”

As for your comments on the Type III, maybe you missed that last line:

The type III virulence system contains homologs of most of these proteins (probably including an axial protein; Cordes et al., 2003), but as discussed previously its phylogenetic position is controversial.

I will concede the comment on the “major flaws,” on the re-read I do see that he clearly indicates he is not adopting the same flaws.  but it appears we have moved from “flaws” to “controversial.”

Irreducibly complex? Not hardly. Myxi, if you want to debate science, it’s not enough to wave around quotes from authorities. You have to research and understand the subject. The appeal to authority works in religion, but not in science.

How ironically amusing that you should make the comment after waving around quotes from authorities to make your case.

Most scientists, and rational people of all stripes, couldn’t care less what IDers believe, any more than we care about flying saucer abductions or golden hemmorhoids.

That doesn’t change the fact that these scientists putting together this model cared a great deal, and specifically said so.  And I shouldn’t have to tell you that a witch hunt most often results in finding a witch.  People generally find what they’re looking for, and quite often simply because it’s the only thing they were looking for in the first place.  They made it very plain, “we want to find something to refute what Behe has said.” 
You don’t have to look very far to find a lot of other people trying to do the same thing.  And it seems odd that if Behe has already been sufficiently countered, that people are going to such great lengths to address his work even now.  I do not agree with you that Behe doesn’t know beans about science, his work is generally seen as a force to be reckoned with, and quite a few scientists are doing all they can to bury it.

The problem is that the “damn antievolutionists� have their own agenda- to insert their religious views into public school science classes.

You might try “RE-insert.”  Apparently you forget which was there first.  Religious institutions had a lot to do with establishing educational systems in this country. 
For my own part, I could care less whether it gets taught as part of science curriculum.  I find it amusing that evolutionists ridicule it on one hand as though it had no merit and nobody could possibly believe it, and on the other hand turn around and call it “pernicious” as one poster has done here.  If it’s as ridiculous as you claim, why concern yourself with it at all? 
I think it would more appropriately be taught, as someone suggested, as philosophy.  And even after going several rounds with several people here who are subjecting it to scientific method, which I have certainly been willing to engage in, it still seems to get ignored here that I have not in any way suggested putting ID on a level plane with evolution at all.  I said it should be taught as an “alternative,” and everyone seems to have automatically assumed that means as an alternative scientific method, which was not my intent at all.  At the time I made that statement, I also mentioned that there were some who approached it from scientific method, giving Behe and Dembski as examples.  That’s when it all hit the fan, and from that point I have been backed into a corner defending Behe’s position as though it were my own.  About the only clear-cut point at which I found myself totally in agreement with Behe was from his insistence that when speaking of being “against evolution,” he is speaking of the ultimate ramifications of it as it relates to origins.  Someone has suggested to me that that would more appopriately be in another field, abiogenesis.  I was simply going on the statement I quoted from Behe, where he says this and still refers to it as evolution, and so I did as well.

But the main problem here is that you obviously think it takes a complete, corroborated description of the evolution of the flagellum to disprove Behe. Not so. Of course, a plausible model of how it could have happened, which is all Matzke is proposing, tends to cast doubt on Behe’s claim that the flagellum could not have evolved.

And “casting doubt” is not disproving.  But I seriously doubt whether one even manages to “cast doubt” on anything with a model that is self-described by its author as a “mixed bag,” and in which less than half of the evidence presented has strong credibility.

In either case, why should we listen to anything you say about this?

I’ll say this again, since it appears necessary once again:  I am not the subject.

 

No, Mixy, you aren’t the subject, but what you SAY certainly is. You are acting as if people here were saying “Well, why should I believe someone like you, who is clearly short/redheaded/writing from an asylum, etc.” No one here is saying that, or at least most of us aren’t. However, people HAVE said, “Based on the poor understanding of this topic you demonstrated in comment X, I shall approach your comment Y with a grain of salt.” You may not LIKE this line of reasoning, and you may not AGREE with anyone’s assessment of your abilities, but it is extremely disingenuous of you to portray any evaluation of the logic displayed in your arguments as some sort of nasty, unfair ad hominem.

*A couple observations on the merry-go-round*

• The world is full of kooks who, while not specialists in a given scientific area, challenge specialists with full conviction that they are the reincarnation of Gallileo.  ID is a case where the kooks in question happen to have the support of a popular religion, hence the high profile.
• Everyone makes arguments from authority; the choice of authority matters a great deal.  If your authority is not a specialist in the area in question, and disagrees with the vast majority of specialists who have spent their lives there, he/she must present evidence, not conjecture.
• Saying “could not have” is not evidence, it is conjecture.
• Showing a way that it “could have” is sufficient to render the above conjecture moot.  It is not necessary to demonstrate “how it did”. 
• When ID has presented a testable, falsifiable hypothesis, has been confirmed by huge amounts of data from interlocking scientific specialties, and demonstrated predictive ability that can be used in new inquiry and the development of new technology - that is when it has risen to the level of a scientific theory - it will be welcome in the classroom.
• Evolutionary theory did all that stuff before it made it into the classroom.
• The hoo-ha about ID is not so much the idea as the insistence that it be allowed to run around the hurdles and go directly to the textbooks of our children.  It’s the running-around-of-the-hurdles that is the problem here.  It elevates conjecture to the level of science; and science has given us so much, we don’t want to trade it for conjecture.  Conjecture is not an “alternative” to a scientific theory.
• I’ve noticed ID proponents and more honest creationists now admit to evolution within a species (hard to deny because it is so obvious).  Well, take a species.  Make a change.  Make another change.  Make another.  Repeat.  After enough changes, eventually you have a different species, Duh!
  So, ID people, get cracking.  You have a lot of work to do.  Your journey begins in the laboratory, in the field, in peer-reviewed journals, in conferences of working scientists; NOT IN THE CLASSROOM.

How can I make this clear?  Myxi, you say (of Matzke)

If he drew nothing from Rizotti’s earlier work, then why would he introduce his concluding paragraph on Rizzotti (and actually on that entire section) with

it is now time to see if Rizzotti can be improved upon. { “Improved upon� implies building upon the foundation Rizzotti supplied, while tweaking it for the flaws he sees in it.}

Myxi, I assume you mistakenly included your interpretation of what Matzke meant {in brackets} in the quote.  Because that’s all it is- “improved upon” can also mean “Tommy, 2+2 does not equal 5.  Let’s see if you can’t improve upon your answer.”  But I don’t know and you don’t know what Matzke meant by that.  I suspect, though, he was following the time-honored tradition of honoring those who have come before.  That’s all speculation, however.  Whatever the case, the point is, and what I said is, that contrary to what you said, Matzke’s model does not draw support from Rizzotti’s, and that’s why I assumed you hadn’t understood the paper or were quote mining.  I stand by that.
Then you say

The puzzling thing is that you would attempt to suggest that “previous attempts to explain flagellar originsâ€? should be taken to mean that everything he says under the heading gets discarded or is worthy of no merit or consideration, or whatever it is you seek to imply.  Any researcher worth his salt will ALWAYS take into account the work that has been done in the field before him.

More of the same.  I implied nothing.  You are the one who said Matzke’s paper was

...based primarily on a study with “major flaws,�

My conclusion, that Matzke’s model was not “based primarily on a study with major flaws”, came from reading and understanding Matzke’s model, not on making assumptions about how researchers worth their salt work.

You say lots more stuff about how important Rizzotti was to Matzke, how long the section devoted to him was, etc.  Doesn’t change the argument one iota.

And then you tell me how I should have made my case.  No thanks- I’ve already done so.

And now we come to the Bizarro world.  You say

I will concede the comment on the “major flaws,� on the re-read I do see that he clearly indicates he is not adopting the same flaws.

Wtf?  So now you concede a point you’ve been wasting my, and your, time over for the entire contents of my 19” monitor?  What was the point of the whole rigamarole, then?  Sheesh.  Enough for now.

Time for the daily reminder…

Myxi visited this site with the claim that ID is somehow superior to evolution. It’s his claim and he’s the guest, so the burden of proof rests on him.

He expends a lot of effort defending the well-known IDolators, but has so far willfully refused to state what he understands ID to be; I lost track of how many posters asked him on how many occasions to do it. Given that his grasp on evolution is shaky, it seems more than reasonable to establish a common understanding of what this debate is all about - after all, his understanding of ID may be similarly flawed and he would best further his cause by removing himself from the debate.

My conjecture is that he refuses to explain what ID is for a simple reason - the debate would be over right then and there, with ID being exposed as a glorified version of the argument from ignorance and entirely without scientific merit.

While it should be straightforward enough to summarize the concept of ID, he expends a lot of effort on defending points that the IDolators made. While some may enjoy to pick apart creationist claims, before one goes there it remains to be shown that there’s a there in the first place.

Part two.  Myxi, you then go on to quote Matzke’s evaluation of his model, and you list his 30 structural components in order of his confidence in them.  At the end of your post, you say

But I seriously doubt whether one even manages to “cast doubt� on anything with a model that is self-described by its author as a “mixed bag,� and in which less than half of the evidence presented has strong credibility.

Well, Myxi, you are not really in a position to judge how well this model fits the facts, if you grade it like a spelling test.  If the statistics (derived from known limitations of protein synthesis) show that even a few of the homologies are good, the confidence in the bulk of the model might well be high.  But I don’t know enough to judge, and you don’t either.

But as I said, that’s not where ID fails anyway.  The discovery that the Type III virulence system (using Matzke’s terminology) is homologous to the base of the flagellum, as I said, demolishes the “irreducible complexity” of the flagellum.
Bedtime.

You might try “RE-insert.â€? Apparently you forget which was there first.  Religious institutions had a lot to do with establishing educational systems in this country. 

Wrong. Very wrong. Just because some of the people who began establishing the public education system when the country itself was being established had religious views, it does not even come close to following that the religious psychos of today have any authority to ensnare public education today with their warped views of the world.

And regarding our dear friend Myxi, all I’ve got to say is, if you ignore something long enough, it just might go away. (S)He’s shown than s(he) has no interest in arguing, as there is a difference between arguing a point for its own sake and beating a long-dead horse that probably never lived in the first place, and which most people here quite rationally don’t believe existed (please excuse my awkward metaphor; I think you get the point). Think about it, people.

Myxi, I assume you mistakenly included your interpretation of what Matzke meant {in brackets} in the quote. Because that’s all it is- “improved upon� can also mean “Tommy, 2+2 does not equal 5. Let’s see if you can’t improve upon your answer.� But I don’t know and you don’t know what Matzke meant by that.

Agreed on the point you made about what it could mean.  But context will always confirm or refute claims about a definition either way, and what he meant was retain what was valid from Rizzotti, assess the flaws and avoid them, and proceed from there to improve upon it.  This is pretty much confirmed by the fact that a chart of three different systems (Figure 4: Systems with components homologous to flagellar components.) has Rizzotti’s model included (4b).  Please understand that in saying he “builds on Rizzotti’s model,” I am not declaring or even implying in any way, that he builds only on Rizzotti’s model.  But of all the previous models he discussed, it was clearly the one he accorded the bulk of his attention, for whatever reason. 

Whatever the case, the point is, and what I said is, that contrary to what you said, Matzke’s model does not draw support from Rizzotti’s, and that’s why I assumed you hadn’t understood the paper or were quote mining. I stand by that.

It’s clear from reading the entire article (charts included) that he not only references Rizzotti, he builds on what Rizzotti has done, as well as the work of others.  It would be very strange for Matzke to dismiss Rizzotti’s work in section 2 and immediately proceed to chart it in section 3 as he continues.  So I stand by what I have said.

My conclusion, that Matzke’s model was not “based primarily on a study with major flaws�, came from reading and understanding Matzke’s model, not on making assumptions about how researchers worth their salt work.

(1) Check my reply again.  I retracted the idea about “major flaws.”  He did indeed reference, and then build upon, the work of Rizzotti, but only after stating the flaws and charting a course that did not make the same errors.  But the F1F0-ATP synthetase model is the one Rizzotti presented.  He charts Rizzotti’s model of it in Fig. 3, and a later (and I assume improved) version of it (Capaldi and Aggeler, 2002) in Fig. 4b.
(2) I made no assumptions about “how they work.”  If they don’t work that way, enlighten me as to how a scientist maintains any credibility while ignoring the work of others.  That is, after all, one of the raps people try to hang on Behe, so it is a natural inference from such accusations, that researchers don’t work that way.

And then you tell me how I should have made my case.

Apparently you were offended by what you assumed was my intention.  I apologize if anything in my response gave you that impression, I assure you that was not the case—I’m doing all I can to wade through the personal remarks and persuade whoever I can to focus on the topic, not me, not fundamentalists, not “worst case scenario” anecdotes that add nothing to anyone’s argument.  My comment had nothing to do with you and everything to do with heading off unnecessary personal comments.  I thought a frank admission on a point which I had missed might serve to aid in the effort for genuine dialogue.  Even if it does not, it is always worth the effort, IMO.

An afterthought on the last post:

“Tommy, 2+2 does not equal 5. Let’s see if you can’t improve upon your answer.�

And at that point Tommy takes the eraser and obliterates the entire thing and starts over? 

Hardly.  He will simply erase the “5” and rethink the problem.  This would be a more apt description of what Matzke does with Rizzotti.

Wrong. Very wrong. Just because some of the people who began establishing the public education system when the country itself was being established had religious views, it does not even come close to following that the religious psychos of today have any authority to ensnare public education today with their warped views of the world.

The response addresses something I never intended, of course.  Someone was making the suggestion that trying to find a place in the science curriculum for any view of religion constitutes an “insertion.”  My point was that when evolution came into the curriculum, it was by the same route of “insertion”—into a system that had no problem with religious views and in fact had views that were probably primarily religious. 

Your response is full of value-judgments that were not a part of what I said.

[quote:  ulfrekr]No, Mixy, you aren’t the subject, but what you SAY certainly is. You are acting as if people here were saying “Well, why should I believe someone like you, who is clearly short/redheaded/writing from an asylum, etc.â€? No one here is saying that, or at least most of us aren’t.

You’re right, most of them are too busy ranting about fundamentalism.  But at least when they do, they aren’t hammering on me, since I’ve never been one.

However, people HAVE said, “Based on the poor understanding of this topic you demonstrated in comment X, I shall approach your comment Y with a grain of salt.�

Gee, you sure are generous with your evaluation.  Are you sure you’re talking about the same thread?

You may not LIKE this line of reasoning, and you may not AGREE with anyone’s assessment of your abilities, but it is extremely disingenuous of you to portray any evaluation of the logic displayed in your arguments as some sort of nasty, unfair ad hominem.

Oh really?  It looks more and more like you haven’t been reading this thread.  I don’t really have to “portray” anybody’s evaluation at all, they’ve done a neat job of it already, from the minute I posted comments.  For instance, the first reply to my first post:

While I won’t imply you’re stupid, I will say you’re gullible and not intellectually honest enough to go look at both sides.

That was a neat trick, implying I’m stupid by stating he wouldn’t imply it.  But I’m gullible and dishonest too.  Oops!  I forgot, how disingenuous of me to make such a comment. 

It didn’t get any better from that point.  A few examples (there were many more):

1) Now I know you’re on crack.
2) Or maybe you’ve forgotten that science has its own “Piltdown Man?�
How could we forget. Ignorant people won’t let us live it down.
3) I have to wonder what you’ve been smoking.
4) I’d just like to mention before the silly boy with the unspellable username posts again
5) In the end you can believe whatever you want, but then I’m free to believe you’re an idiot for your beliefs as well.
6) It just seems to me that you are whining.
7) It’s idiotic statements like the ones you’ve made here that make it clear you’re talking out of your ass
Gee, for a minute there I thought I was being accused of being on drugs, ignorant, silly, an idiot, a whiner, and talking out my ass.  But that would be disingenuous of me to notice they were saying that, wouldn’t it?

Sexy Sadie, you have won my heart.  I shall not waste any valuable electrons (or their distant tangential relative in the continuum, time itself) answering our visitor Mxy.

Hold on guys and gals. Please stop ganging up on Mxzy. I have something to say and it’s really important so please read everything carefully. I know we’re all tired after putting so much hard work and thought into our posts, trying to reach a consensus that satisfies people of faith and athiests alike, but this is really really important that I share this with you now. OK?

Mxyzptlk:

You’re right.

Regarding Les’ suggested read, Evolution in (Brownian) space: a model for the origin of the bacterial flagellum Copyright 2003 by N. J. Matzke Preprint Version 1.0 (last updated November 10, 2003) - you wrote:

“There was an agenda before they even began, to try their best to find something to counter these damn “antievolutionists!”

Let me go back and check if I’m misquoting you…nope, that’s it. And let me say that I agree completely. Matze’s work is, at best, a hoax. As you say, it’s a:

“mixed bag,� unavailable “structural information,� “not very balanced?�

Did I get that quote right? Let me check. Yep. And you are so right! Especially about the “mixed bag”! Why didn’t I see that earlier and discount his work immediately?

I don’t care what warbi, Les, zilch, Consi, elwed and Ulf had to say over the last couple days about your points. That mean stuff is best left unaddressed because it’s too basic to trifle with now that you have laid your cards on the table for us to see what you really know about ID and Behe. Read ‘em and weep, ladies and gents. Me and Mxyzptlk will be taking our winnings now.

We have bigger fish to fry anyway, like that “controversial” phylogenetic position (Be warned, the source is Wikipedia, so it’s a little *******LIBERAL******* guys.)

We’ve got work to do Mxyzptlk. Can’t let those evolutionist scientists decide too much on their own about what the truth is about all those gaps in their unproven theory of origins. Mxzy, for the life of me I can’t understand why they don’t suddenly get it like I do now. It’s so obvious. And important. And all along I denied it.

Best of all *giggle* this is just one example of one of many kinds of arguments and cosmological things that evolution cannot explain fully. Once again they have failed to debunk Behe’s basic premise, which you have rightly relied on throughout this discussion.

You know what we need to do? You need to email me offlist so we can get started working on a document - which we will spread as widely as possible to anyone who wants it and even some who don’t - that will spell out exactly how to win an argument against an evolutionist scientist ... just like you have just done with VoijaRisa. It doesn’t stop there. We’ve got some fundraising to do so we can get some serious numbers on our side with a well managed PR campaign. After all, even Darwin must have done some lobbying to get his theory into textbooks back in the Dark Ages. Fairzies, right?

...Now where would we find some people willing to donate money for a plan as grandiose as this?

Can’t waste time debating evolutionists all day. We need a plan of attack…kinda like what the Discovery Institute did with the Wedge Document, but maybe with a little less biology in it because that’s not really my specialty. Is it yours? Seems like you have a taste for it what with all the Behe you’ve quoted for us on this thread and especially that analysis you wrote after reading Matze’s work. (“Mixed bag” - I’m still embarassed I missed that one after reading Matze’s article twice yesterday…)

Can I be frank though for a moment ... I fear my emotions are getting the best of me in this moment of raptu…er…clarity and the fools here will just make fun of me and never let me come back. I’m too excited and plus my hands need a rest. Hang on.

**4 minutes pass**

OH! OH! OMG I was just taking a dump and I just had the best idea ever, which I need to tell you about now. Check it out: What if we…like…help Behe get hooked up with a consulting gig with these guys for next year’s print run. (I don’t want to say more here and get SexySadie riled up. Email me and we can work out the details asap while they are still putting together the content for the science books!!!!!!!)

*Hang on, I just re-read your previous post, and now I’m thinking maybe you wouldn’t like that to happen. (Behe’s ideas in textbooks, I mean.) I’m so embarassed and confused that I am possibly misunderstanding you. We want an “alternative” view presented, right? Otherwise how will the kiddies know enough to form an unbiased opinion about the limits of science?

I just wanted to directly address some MainStreamMedia nonsense Les was going on about maybe 40 posts ago which you might have missed because I don’t think you directly addressed it…Namely that what Les doesn’t know (and what we do) is that Behe will be vindicated in the end no matter what the MSM writes about him. Les wasn’t there at the Dover Trial - prolly only reads MSM evolutionist apologist crap off Google News. People, bear in mind: Dover ain’t over until John E. Jones III says it is. I really think the New Year will hold some surprises for these fools.

I can’t believe I used to buy into the obvious agendas of these evolutionist liars. (Trouble is there are so many of them. Don’t worry. We’ll change that.)

And heck, with an agenda as big as they have on this thing ... just what might they be capable of doing to further their unverifiable theories about the origin(s) of life? Honestly, it doesn’t matter, because Dembski’s got us covered with the master plan. Hint: check out the Vise strategy. We can talk about it later after you’ve had a chance to properly absorb it - but trust me - this guy’s good. I think you’ll really like the part where he says the evolutionists shouldn’t get to ask any questions. Surefire. Hit me up high, bro. We’ve got this one wrapped. Proven.

“not very balanced?�

You got that right and I’m glad you just proved it to me, too. You know the funny thing - the answers were there all along and I was just choosing to ignore what you had written.

Boy am I glad I got on the bus before it was too late to make a difference in this thing. It would have been insanity to have ignored a real working scientist like Behe - especially his work from before the mainstream media got hold of it and started distorting and categorizing his true meaning.

(Also, which Bible College did you attend? I would very much like to learn more about their curriculum and perhaps enroll my children there in the future. Anyway, please email me so we can get to work on this right away.)

But as I said, that’s not where ID fails anyway. The discovery that the Type III virulence system (using Matzke’s terminology) is homologous to the base of the flagellum, as I said, demolishes the “irreducible complexity� of the flagellum.
And as I pointed out already, quoting from Matzke’s own comment about it,

The type III virulence system contains homologs of most of these proteins (probably including an axial protein; Cordes et al., 2003), but as discussed previously its phylogenetic position is controversial.

You simply cannot assert your position as a dogmatic certainty (“demolishes”) when the author of the study himself says of the type III virulence system upon which you base your claim, “its phylogenetic position is controversial.”
TO EVERYONE ELSE:  I apologize for repeated material, but this particular inividual keeps ignoring facts I pointed out earlier.