Congratulations are in Order
by MikeGeneChecked the blogs today and I was pleasantly surprised to see that Nick Matzke was the co-author of a new paper about the evolution of the bacterial flagellum. Congrats to Nick! It's kind of fun to watch this unfold, as I remember the good ol' days when Nick first started arguing about the flagellum back on the ARN forum. Needless to say, I think this is the first published article that attempts to tackle the origin of the flagellum and, although I have yet to read the paper, I am confident that it will be quite helpful in bringing a higher resolution focus to this issue.
September 7th, 2006 at 11:21 pm
Congratulation Nick!
Salvador
Comment by Salvador T. Cordova — September 7, 2006 @ 11:21 pm
September 7th, 2006 at 11:24 pm
Boooo!
Comment by Douglas — September 7, 2006 @ 11:24 pm
September 8th, 2006 at 9:11 am
Excited to read it. Nice work, Nick.
The abstract sounds like a solid attempt to address the issue.
Comment by Doug — September 8, 2006 @ 9:11 am
September 8th, 2006 at 12:27 pm
Why?
Comment by chunkdz — September 8, 2006 @ 12:27 pm
September 8th, 2006 at 5:13 pm
Nick Matzke is making an attempt to answer the questions that Behe criticized Dr. Russell Doolittle for; that, and N.Matzke is doing it through the appropriate channels.
I currently believe the BF to be an example of IC; but if N.Matzke can present a compelling case that stands up to scrutiny we should be more motivate to accept his findings - assuming our objections to the BF's possible evolutionary origin were for reasons that did rest on empirical evidence.
Comment by Doug — September 8, 2006 @ 5:13 pm
September 10th, 2006 at 4:26 pm
Mike Gene:
The abstract doesn't give as much reason for optimism as Mike does. But he did always have a soft-side for Nick.
Comment by Bilbo — September 10, 2006 @ 4:26 pm
September 11th, 2006 at 9:55 am
Hi Bilbo,
If we trust what the abstract says we shouldn't really doubt that Nick Matzke makes an attempt to avoid 'conceptual leaps'. I don't know of any good reason for doubting the abstract.
Comment by Doug — September 11, 2006 @ 9:55 am
September 11th, 2006 at 11:32 am
Matzke didn't think that Darwin's explanation of eye evolution had any major obstacles, why should he think that flagellar evolution is a "conceptual leap"
His argument has always rested on the pillar of homology, yet he doesn't consider two unique and indispensible proteins that have no homolog (even by his relaxed standard) to require a conceptual leap.
Matzke doesn't consider anything to be a great conceptual leap where Darwinism is concerned. Don't expect that this will change just because he is published.
Comment by chunkdz — September 11, 2006 @ 11:32 am
September 11th, 2006 at 1:35 pm
First off, congrats to Nick for getting something published. It isn't easy to accomplish, so good show, Nick!
From the abstract:
I find that last sentence rather interesting. Without having read the full article (because I can't get it), the indication here seems to be that all this paper really does is attempt to "speculate" (interesting word choice in itself) on how research into the issue of flagellar evolution might look. In other words, this paper itself isn't presenting any actual lab results that would lead us closer to a detailed, testable model of how the flagellum evolved.
Even more interesting, though, (if one reads between the lines), is the implication here that no such experimental programs have existed to date, or if they have, they have not been successful. That would seem to fly in the face of all the claims that the evolution of the flagellum is a problem long since solved by biologists. Indeed, I have often seen long lists of research studies posted on blogs and around the net that supposedly demonstrate the detailed, testable model of flagellar evolution. Apparently, either Matzke and Pollen are unaware of all these research studies, or all those oft cited studies really don't provide the model as claimed. If its the former, they are in good company as Behe himself was accused of not being aware of them when he wrote Darwin's Black Box. If the latter, then several biologists and other participants in internet disussions are grossly misinformed.
Either way, though, the abstract seems to be a pretty strong indication that in the 10 years since Behe's book was published, evolutionary biologists have still not solved the riddle of flagellar evolution in Darwinian terms, nor has a detailed, testable (and potentially falsifiable) model been developed. Further, it seems to also be the case that there really hasn't been any detailed structure as to how a biologists would even go about conducting the experimental research, since this paper offers "speculations" as to how such research "might" go.
To me, this looks like a frank admission that no one has a clue how the flagellum evolved, which is exactly what Behe claimed in his book, and for which he has endured 10 years of mocking and excoriation from Darwinists. Matzke and Pollen are to be congratulated for being honest enough to admit that Behe was right after all.
Comment by DonaldM — September 11, 2006 @ 1:35 pm
September 11th, 2006 at 11:35 pm
To DonaldM,
You have an interesting reaction to the news that Behe's flagellum challenge appears to have been accepted.
As for the last 10 years"¦ it has taken a while to separate the grain from the chaff. The back-and-forth papers has caused Behe to redefine his terms and two of his three alleged IC systems (blood clotting and eyes) have been demonstrated as indefensibly weak. Therefore, while there will always be never-say-die advocates for all of the systems, it looks like scientific forces have focused on the star of the Dover trial and the No Free Lunch's cover art, the Bacterial Flagellum.
Rejoice! This is how science is done.
What did you expect? Did you think everyone would just agree "Yep, that's designed alright" and leave it at that?
Here is a worst-case scenario (for ID). Some energetic individuals will sit down and catalog the Flagellum's proteins to create "a model of flagellar evolution and speculate as to how an experimental programme focused on this topic might look." (Pollen and Matzke abstract, 2006) This published paper will be reviewed (with a fine-toothed comb) to iron out weaknesses. After surviving the gauntlet, predictions will be made and experiments performed. The experimental results will be reviewed against the predictions. Any surprises will be folded back into the model and experiments ran again. Each step providing insight into how natural processes could have created the Flagella. The never-say-die advocates will dismiss all this as meaningless while the rest of the scientific community will eagerly make use of new knowledge.
What would be the best-case scenario? This becomes a total waste of effort because the Flagellum required an unknowable creator and, therefore, is beyond our capability to understand how it was created. In other words, pursuit of knowledge is worthless; we should just accept the truth and be happy with that?
Given a choice between trying to obtain my own knowledge, or being given someone else's truth, I will die trying.
Comment by Thought Provoker — September 11, 2006 @ 11:35 pm
September 12th, 2006 at 4:24 am
It is your perception that the evolution of blood clotting and eyes has been documented. The arguments have predictably relied on identifying homologous proteins for some of the relevant proteins and assumed the adaquacy of vaguely described theoretical pathways.
Here is a worst-case scenario (for ID). Some energetic individuals will sit down and catalog the Flagellum's proteins to create "a model of flagellar evolution and speculate as to how an experimental programme focused on this topic might look." (Pollen and Matzke abstract, 2006) This published paper will be reviewed (with a fine-toothed comb) to iron out weaknesses. After surviving the gauntlet, predictions will be made and experiments performed. The experimental results will be reviewed against the predictions. Any surprises will be folded back into the model and experiments ran again. Each step providing insight into how natural processes could have created the Flagella. The never-say-die advocates will dismiss all this as meaningless while the rest of the scientific community will eagerly make use of new knowledge.
Why not look forward to a genetically engineered organism deprived of genes coding the constituent proteins and placed under selective pressure to see if the proteins evolve? Models authenticated by experimental results, rather than by clever stories, would be refreshing indeed.
Comment by Bradford — September 12, 2006 @ 4:24 am
September 12th, 2006 at 10:54 am
Only if you misrepresent what Behe was claiming were IC components of the blood clotting cascade. I can't find the link, but Guts already showed that the criticisms against Behe's claim falls flat because the critics state that Behe asserted certain factors being IC when in actuality he didn't. Then the critics show how a particular animal exists without these factors…. thinking that they proved Behe wrong. But the problem is that these components were never claimed to be IC by Behe.
Comment by Doug — September 12, 2006 @ 10:54 am
September 12th, 2006 at 11:04 am
Who said the creator was unknowable? All I have ever heard asserted was that certain characteristics of the Creator can't be definitely assumed with finding an item with the hallmarks of design. That doesn't mean that there wouldn't exist other avenues, independent of just the flagellum, to help discern more about this Creator.
Also, what are you defining as the pursuit of knowledge? Does a particular item only count as knowledge when it is reducible to something else? If so, why?
Comment by Doug — September 12, 2006 @ 11:04 am
September 12th, 2006 at 11:36 am
Thought Provoker
Even more interesting is that its taken 10 years for that happen, apparently. YOu completely missed the point of my post which is that not only was Behe correct ten years ago when he said that no research studies existed that provided the detailed, testable (and potenially falsifiable) models in Darwinian terms for the evolution of any of the IC systems he described in Darwin's Black Box, but also that it is now ten years later, and that is stillthe case. Worse, as Matzke and Pollen tacitly admit, no one has even offered a viable experimental framework to conduct experiments to create such a model. Hence, N & P can only "speculate" as to how research into the question "might" go.
No, science is done as Bradford just suggested:
PT:
Based on this comment, I would suggest you spend a little time reading up on eplistemology. The idnetitiy of the designer is an interesting question, but is completely separate from determining whether or not something was/is designed in the first place. Perhaps you might read William Dembski's The Design Revolution to gain a better understanding of these issues.
Comment by DonaldM — September 12, 2006 @ 11:36 am
September 12th, 2006 at 11:56 am
Considering that self-proclaimed "open-minded" individuals are often among the most closed-minded of individuals one can encounter — you know the sort: your reasons for declining to believe what they want you to believe are always waved away as but proof of your "closed-mindedness," which you can, of course, overcome only by accepting their beliefs — is it really that much a surprise that a "Thought Provoker" can't?
Comment by Ilion — September 12, 2006 @ 11:56 am
September 12th, 2006 at 1:14 pm
Excellent point, Troy D.
Comment by derwood — September 12, 2006 @ 1:14 pm
September 12th, 2006 at 2:47 pm
Has anyone read Nick's paper yet?
It's bothersome to see so many critiques about it just based off of the abstract.
Comment by Doug — September 12, 2006 @ 2:47 pm
September 12th, 2006 at 3:55 pm
DonaldM wrote:
If thats all Behe claimed in his book, its nothing but a gap argument, and I don't know what the fuss is about. I thought that the whole point of a system being IC was that it couldn't evolve, or at least that it was extremely unlikely to. He's been mocked for ten years because its not particularly difficult to show how an IC system could evolve, especially since incomplete flagellum exist now and work just fine; how flagellum actually evolved is something else, since it occurred hundreds, if not thousands of millions of years ago in extremely small organisms with no hard parts.
Comment by Aagcobb — September 12, 2006 @ 3:55 pm
September 12th, 2006 at 4:19 pm
You are in no position to declare a lack of supporting data results from our ignorance of it. It may very well result from the non-existence of such data.
I thought that the whole point of a system being IC was that it couldn't evolve, or at least that it was extremely unlikely to. He's been mocked for ten years because its not particularly difficult to show how an IC system could evolve, especially since incomplete flagellum exist now and work just fine;
It is not difficcult to "show" anything if imagination is the source. Behe's point, which is missed by his opponents, is that the claimed evolution of such multi-component systems is theoretically but not empirically supported.
how flagellum actually evolved is something else, since it occurred hundreds, if not thousands of millions of years ago in extremely small organisms with no hard parts.
How indeed since the point of Behe's position is that intelligence is a causal component of natural history events.
Comment by Bradford — September 12, 2006 @ 4:19 pm
September 12th, 2006 at 4:58 pm
Thanks for the compliments folks. We are lobbying NRM to see if they will make the article free for the benefit of everyone. This is more likely after the print version comes out in October I think. But I do recommend reading the article if possible ;-). A backup option is to visit a local university library with a thumb drive, I have found that most computers at universities now have USB ports and you can suck down articles to your thumb drive.
I have responded to critiques, such as they are so far, over on PT, which is where I will conduct most arguing. Brief responses to points here:
(a) I would concede that it's basically true that "no one had a clue" about flagellum evolution when Darwin's Black Box came out in 1996. Only one or two short discussions of the matter existed back then. Virtually all of the homologies and other relevant work have been published only in the last 10 years since then. However, this really wasn't true for Behe's other main systems, i.e. the immune system, blood-clotting, and the cilium.
(b) If your real beef is that you have issues with homology indicating ancestry, then you have bigger problems than I can help you with. Suffice it to say that homology as determined by BLAST and PSI-BLAST (search the NCBI website) is an absolutely standard technique used probably millions of times a day by researchers around the world.
(c} Contrary to popular belief, the homologies identified in Table 1 of the paper are much more conservative than the homology discussions in my 2003 online essay. At most only a handful of the identified homologies could be considered "subjective." See further discussion in the PT comments.
(d) This thread has yet more examples of the very common phenomenon of naive talk about experimental evolution of the flagellum. IMO demanding that scientists "evolve the flagellum in a lab" is almost as ridiculous as asking them to evolve bat wings in lab mice. If you think carefully about it there are some important roles that experiments can play in testing evolutionary models (some of which we outline in the paper), but the silly creationist demand to reproduce millions of years of evolution in the lab is nothing more than simplistic rhetoric.
(d) It's "Pallen", not "Pollen".
Lastly: Once people get around to reading it, it is worth keeping in mind that this article started out as a "Science and Society" essay. Under the pressure of reviewers it essay got more and more science-y, in part because the definitive review has not yet been done so we had to fill in details with things like the Big Homology Table, but it is not the full review monograph that needs to be done in the near future. Here, we are just trying to give people the big picture, show that the ID guys get some crucial and obvious points wrong, and outline the major points that the probably any specific evolutionary hypothesis will incorporate.
A really thorough review would probably be twice as long as the Matzke 2003 essay with major updates and much more technical analyses of homology etc. so it is not a trivial matter to pull off. I don't think that even this would impress creationists who typically demand infinite detail from evolution while providing no more than "poof" themselves, but there is an awful lot that can be said even at this early stage of investigation.
Watch the PT blog in the next few weeks where I intend to expand on some of the points in the paper. Mike Gene has undoubtedly figured out by now (if he didn't see it back in April) that another paper by Pallen published earlier this year strongly supported my highly controversial T3SS-ATPase homology hypothesis from 2003. I fully intend to crow about that in excrutiating detail over on PT at some point soon — particularly since Mike Gene's major response to my essay was to critique exactly that hypothesis on the basis of IC — but I would be interested in whatever comments he has before that.
Comment by Nick Matzke — September 12, 2006 @ 4:58 pm
September 12th, 2006 at 5:08 pm
aacobb wrote:
I never claimed that that was all Behe wrote. I merely made the point that Behe was right in tha there was not 10 years ago (nor is there now) any research studies in peer reviewed journals that provide the detailed, testable (and potentially falsifiable) models that explain how any of the IC systems Behe described in his book came to be through Darwinian pathways. None. Of course, Behe said more than that and, no, it isn't just a "gap" arguements. As far as I can tell, the criticism of ID being merely a "gap" argument implies that that gaps in question are details to be filled in through naturalistic explanations only. Intelligence can not be included. That belies a hidden presupposition of naturalism, which I believe to be misguided.
Comment by DonaldM — September 12, 2006 @ 5:08 pm
September 12th, 2006 at 5:12 pm
DonaldM, you are wrong. Read this and this. You're not even in the game unless you can put forward a serious rebuttal of why this is wrong.
Comment by Nick Matzke — September 12, 2006 @ 5:12 pm
September 12th, 2006 at 5:22 pm
Nick writes:
It should in fairness be pointed out that the 2003 Matke paper Nick mentions was very well critiqued by Dembski in this article: Biology in the Subjunctive Mood: A Response to Nicholas Matzke. I'll leave it to the reader to decide who had the better arguments.
Comment by DonaldM — September 12, 2006 @ 5:22 pm
September 12th, 2006 at 5:26 pm
Page counting is an argument?
Comment by Nick Matzke — September 12, 2006 @ 5:26 pm
September 12th, 2006 at 7:08 pm
"Excellent point …"
It's a gift.
Comment by Ilion — September 12, 2006 @ 7:08 pm
September 12th, 2006 at 7:45 pm
Nick
That highly disingenous of you, Nick. You know full well that Dembski himself said in his article that the reference to the number of pages wasn't an argument, but a reality check…and he was quite right to say so. The rest of his rebuttal of your article DOES constitute an argument and demonstrates why your supposed detailed, testable model for the evolutionary origin of the flagellum, is nothing of the sort.
Nick
Oh dear me, how could I be so blind and so unawares!. Mea cupla, mea culpa!
Nick, which part of "detailed, testable (and potentially falsifiable) is unclear to you? Not one of these articles or books provides such a model. Most offer at best more of the same on protein sequence comparisons. That is not the model that's required. DO you really think that if any of the cited references to which you refer actually provided such a model that Behe himself would not be the first to be pointing them out? Once again you demonstrate why Dembski said of you in his article:
You're the master of the literature bluff!
Comment by DonaldM — September 12, 2006 @ 7:45 pm
September 12th, 2006 at 8:30 pm
Hi Nick,
Actually, as I mentioned before, this is a bad time for me.
I'll definitely check out your PT blogs on this issue, but please don't expect some type of 'rapid response.' I have indeed read your paper and will eventually reply (but not in any direct fashion; I'll deal with the origins question and will, of course, have to acknowledge/consider your hypothesis in the context of the overall argument). In fact, if all goes as planned, after all these years, I should finally be making my case about design and the flagellum in chapter 7 of TDM vol II.
P.S. I may be able to address one of the tangential aspects of your paper this weekend.
Comment by MikeGene — September 12, 2006 @ 8:30 pm
September 12th, 2006 at 9:32 pm
Nick:
Speaking of which…
Now that's detailed, testable, and it pretty clearly puts to rest one ID-related claim.
A question for the front-loaders here (um, not the tractors ….) - when did the front-loading for the bacterial flagellum occur? With the inception of the F1-ATPase, or with the "creation" of its simpler evolutionary predecessors? How does one experimentally distinguish between these two hypotheses (or any others pertinent to the issue)?
Comment by Art — September 12, 2006 @ 9:32 pm
September 12th, 2006 at 9:59 pm
To all,
Thank you all for your responses to my submission. I hope you don't mind that I lump my replies into this one post. Now that Nick has replied, some of this may have been overtaken by events.
Bradford wrote:
That is not what I said, and it is not my perception. My suggestion is that compared to the Bacterial Flagella the blood clotting system and eyes were weak examples of Irreducible Complexity. I will go into more detail later.
Bradford asked…
Because that is essentially trying to prove a negative. How long do we wait for the negative to be "proven"? Even if the experiment has a positive result, we wouldn't know why. Little knowledge would be gained. While this experiment invokes interesting politics the reality is that, unless the Intelligent Design proponents are covering the costs, they have no room to complain about when or how this experiment is run. Finally, I think Nick dealt with why it's a poor idea quite well.
Doug wrote…
Was this the link you were looking for?
http://www.arn.org/docs/behe/m...
Compare this to the Bacterial Flagella. The Flagella system is complex and well defined. We know the 40+ protein structure that makes up what Behe is calling an Irreducibly Complex System and we have a reasonable idea of what it would take to refute the claim. Can you say the same thing about the blood clotting system? If you can, please do so or provide a link.
Doug asked…
Excuse the misunderstanding. I should not have implied the alleged creator was unknowable. My intent was to understand what would be considered a desirable outcome of the proposed experiment to others. What would be the "best case" results for ID? What knowledge would these results bring, if any?
Doug asked…
The understanding of the mechanisms. laws, etc that helps explain the natural world we live in. My test threshold of understanding is the ability to communicate information to unbiased observers and have them reach the same conclusions.
As to your follow up questions, yes I believe this pretty much means that pursuit of knowledge ends up reducing thing to their simplest components. This enables the knowledge to be communicated to others.
DonaldM said…
You are right in that I did not address this obvious point you were trying to make. But since you have pressed it…
How dare you vilify and trivialize an entire field of study because they didn't hop to your whims. Ten years ago, Behe became a senior fellow of the Discovery Institute's Center for the Renewal of Science and Culture. That same year, he published Darwin's Black Box. By Behe's own words the book was targeted to "a general audience", not scientists. Included in his book was the following definition of Irreducible Complexity…
"By irreducibly complex I mean a single system which is composed of several well-matched, interacting parts that contribute to the basic function, and where the removal of any one of the parts causes the system to effectively cease functioning. (Behe 1996, 39)"
To Evolutionary Biologists, this unscientific proposal was dismissible on its face. However, with the Discovery Institute's help and some judicious redefinitions the target and stakes have changed. The new definition is"¦
"An irreducibly complex evolutionary pathway is one that contains one or more unselected steps (that is, one or more necessary-but-unselected mutations). The degree of irreducible complexity is the number of unselected steps in the pathway." http://www.arn.org/docs/behe/m...
Of course, Behe claims this is what he meant all along, but this is not what was presented 10 years ago, and it was not presented in a scientific forum. Asking for special consideration because this is a popular "movement" is one thing, demanding it is just down right rude.
Ilion wrote"¦
Even though this wasn't directly addressed to me, I will respond.
First of all, I have to smile at the tangled double references you got yourself into. What is it that I "can't" do? Yes, I have some difficulty overcoming disbelief by just accepting what others want me to believe.
It is not my intent to nit-pick your writing style (I have nothing to brag about). However, it does show that stubbornness is a two-way accusation. In this situation we have people actively researching, critiquing, refining and testing concepts. I believe this is a good thing. So, what is it that you want me to believe?
To Nick…
Please excuse my not checking the spelling. It is Pallen MJ, Matzke NJ. (2006). Congratulations. I look forward to reading your paper.
Comment by Thought Provoker — September 12, 2006 @ 9:59 pm
September 12th, 2006 at 10:05 pm
Yeah, that Lane et al. article came out in the last week of the Kitzmiller trial, and Mark Pallen emailed me right around then saying he had reached the same homology conclusions — but he wasn't aware of the Lane et al. article until I pointed it out to him. So two labs with different methods independently reached the same (well, mostly) homology conclusion I had proposed in 2003.
It was an above-average week.
(And, for you skeptics out there, this constitutes a confirming test. My model was therefore detailed enough to be testable, and this is absolute undeniable proof that claims that the flagellum evolution model is untestability are wrong.)
Comment by Nick Matzke — September 12, 2006 @ 10:05 pm
September 12th, 2006 at 10:06 pm
Why would we assume it would take millions of years if environmental conditions are favorable to a rapidly reproducing species? Because it is convenient to the argument at hand? How many generations would it take under suitable conditions?
Similarly structured proteins in organisms containing thousands of them and parallel functions to boot would be expected of design as well. And don't bother questioning whether non-functional intermediates could block pathways to any particular function.
The approach is simple and the outcome not even controversial if all that is required is a BLAST search. Work and effort? Sure. But if the mechanism itself cannot be tested because of time frames, even for unicellular organisms, then the presumption of evolution for any structure need not even be questioned. Just accept it. And they say an ID approach short circuits inquisitiveness.
Comment by Bradford — September 12, 2006 @ 10:06 pm
September 12th, 2006 at 10:16 pm
"Why not look forward to a genetically engineered organism deprived of genes coding the constituent proteins and placed under selective pressure to see if the proteins evolve?"
Because that is essentially trying to prove a negative.
This particular talking point is wearing out. It is potentially supportive data for either side. If the structure in question evolves, or even shows significant movement in that direction, it is a what- positive?
How long do we wait for the negative to be "proven"?
As long as it takes to demonstrate plausibility for abiogenesis. Natural history data is rarely conclusive in any case. The resulting data, when combined with other results, is cumulative. Data can support two possibilities.
Even if the experiment has a positive result, we wouldn't know why.
Why say this instead of explaining that selection enhanced survival?
Little knowledge would be gained.
That is a presumptuous statement in advance of a test.
Comment by Bradford — September 12, 2006 @ 10:16 pm
September 12th, 2006 at 10:38 pm
I am new to the inter-politics of Evolution/ID Blogs. So I may be risking stepping on a land mine here, but I have to relay the following information…
Yesterday, DonaldM made his post both here and on Uncommon Descent (maybe others). I first replied on Uncommon Descent and then copied that reply here. I knew my post would probably be on the controversial side, but I didn't think I crossed the line.
My post never showed up on Uncommon Descent, and today it was announced that I won't be with them any longer. While, it may have been an accumulation of slights that caused the expulsion, I noted the announcement was in the very thread and location where my reply should have appeared.
My long winded point is that Telic Thoughts should be proud that they aren't afraid of some real discourse in their discussion. I am impressed with the interaction so far and will strive to be a polite, but worthy "Provoker" for as long as you will have me.
Thank You and Regards
Thought Provoker
Comment by Thought Provoker — September 12, 2006 @ 10:38 pm
September 12th, 2006 at 11:27 pm
You are right in that I did not address this obvious point you were trying to make. But since you have pressed it"¦
How dare you vilify and trivialize an entire field of study because they didn't hop to your whims.
Vilify and trivialize? Donald stated a fact: "no research studies existed that provided the detailed, testable (and potenially falsifiable) models in Darwinian terms for the evolution of any of the IC systems he described in Darwin's Black Box, but also that it is now ten years later, and that is still the case."
Nick provided the reasons. A supposition that millions of years are required and the sufficiency of homology arguments. There is either no need to test the selection of pathways to IC systems (homology) or no way to do (time frames) it or so it is said. Actually the vilification comes from your side in the form of hurling invective against those unwilling to
accept an untested stochastic process as capable of generating IC in the absence of intelligence.
Comment by Bradford — September 12, 2006 @ 11:27 pm
September 13th, 2006 at 12:23 am
I love how I get accused of bluffing when all of my cards are on the table — e.g. decades of research by hundreds of immunologists with experimental tests confirming the transposon hypothesis for the evolutionary origin of adaptive immunity. Just wave it all away as not detailed enough, and then assert that your own "IDdidit" explanation is equally good.
Behe did exactly the same thing in Kitzmiller. And people wonder why Behe failed to convince the court…
Comment by Nick Matzke — September 13, 2006 @ 12:23 am
September 13th, 2006 at 12:34 am
Because one or a few lab strains does simulate billions of diverse bacterial strains in the wild, petri dishes do not simulate millions of different natural microhabitats in which motility and related processes might be useful, lab population sizes are miniscule compared to microbial populations in the wild, and the length of a research grant does not simulate the length of time available to nature. Experiments are useful hypothesis testing tools, but typically only creationists are naive enough about the role of experiments in science to say things like "demonstrate the whole thing in the lab or I won't believe it and will believe my magical miraculous explanation instead."
Comment by Nick Matzke — September 13, 2006 @ 12:34 am
September 13th, 2006 at 1:07 am
DonaldM wrote…
I interpreted this as Donald calling "Darwinists" people who unjustly mocked an earnest author for 10 years. It seemed to me he was vilifying said "Darwinists". I also felt Donald was showing impatience with them when he said "…no one has even offered a viable experimental framework to conduct experiments…" thus trivializing on-going efforts as being less important than the experiment he wanted conducted.
I may have leaped to some incorrect presumptions of who Donald was talking about and that he really didn't expect that an experiment to have been conducted before now. If that is the case, I sincerely apologize.
Even if I did understand Donald's intent correctly, I agree my comment was still too strong. My lame excuse is that our T1 provider was giving me the run around for three hours. Therefore, I was angry and bored with nothing to do but reply to Donald's blog entry (offline).
Comment by Thought Provoker — September 13, 2006 @ 1:07 am
September 13th, 2006 at 1:54 am
Bradford wrote…
I replied…
Because that is essentially trying to prove a negative.
Bradford rebutted…
I won't argue that the continuous demand for others to conduct a particular experiment in a particular manner is getting old.
However, I presented two responses to your question. The first one was the old. obvious, simple and, I believe, true explaination of why I (and others) aren't interested in conducting your experiment. You, obviously, disagree which is perfectly understandable. That is why I offered the second response. Here, let me repeat it….
While this experiment invokes interesting politics the reality is that, unless the Intelligent Design proponents are covering the costs, they have no room to complain about when or how this experiment is run.
At the risk of being impolite (again), who should foot the bill for this experiment? The people who think it is worthwhile or the people who think it is a waste of time? If Discovery Institute was willing to cover the costs, I have little doubt that there exists an independent biology lab somewhere that would be willing to take the money and perform the experment.
Comment by Thought Provoker — September 13, 2006 @ 1:54 am
September 13th, 2006 at 8:56 am
No, I was referencing a discussion that Guts had on here regarding the blood clotting cascade.
Comment by Doug — September 13, 2006 @ 8:56 am
September 13th, 2006 at 9:29 am
Hi DonaldM
Thats your opinion, and I think history demonstrates its incorrect. For millenium, you teleologists had the field pretty much to yourselves; everything was presumed to be caused by inhuman intelligence. A few centuries ago, people started empirically testing natural explanations, and more progress has been made in understanding how things work since then than was made in the prior 10,000 years of teleological thinking. In contrast, not one single breakthrough in understanding observable phenomenon has been achieved by positing direct intervention by an intelligence other than our own or another large brained, natural organism (tool making chimps, for example). I believe its kind of hard to make the case that methodological naturalism is misguided, with that kind of track record. If you can, I'll be impressed.
Comment by Aagcobb — September 13, 2006 @ 9:29 am
September 13th, 2006 at 10:21 am
Then demonstrate something independent of time constraints. Life cannot be generated or sustained without a mechanism that maintains the fidelity of the replicating process while allowing for selected copying errors. There must be a balance between fidelity and errors. A complete absence of the latter terminates an evolutionary process and too little of the former compromises function. A related prediction is that function enabled by specific nucleotide sequences is lost in the absence of error detection and repair mechanisms. Unless there are existing genes, that code for RNA and proteins required by such mechanisms, genomes decay and become non-functional.
Since error detection and repair mechanisms acquire their selective value based on the prior existence of replicating sequences, whose loss of fidelity would be detected and repaired, an initial genome would be without such mechanisms. Since you have correctly ruled out magical solutions we will rule out the possibility that the specified sequences enabling ed&r genes are generated without a natural selection basis.
Testing is not problematic based on time constraints. Organisms and nucleic acids are readily available. If replication fidelity is fatally compromised in the absence of ed&r mechanisms then
a capacity for open-ended evolution is short cicuited at the outset because viable variants of the automaton process are not possible.
Comment by Bradford — September 13, 2006 @ 10:21 am
September 13th, 2006 at 11:17 am
Bradford wrote:
You took the words right out of my mouth, Bradford. Well put.
Nick's entire argument that some of the IC systems Behe talked about have been explained in Darwinian terms hinges on the homology argument. I find that incredibly weak and bordering on question begging.
Why is that we would observe homologous structures in biological systems if and only if those systems evolved through RM/NS? Why could they not also be evidence for common design? Pointing to similar protein structures around the biological world as proof positive of common ancestry is weak. It is also untestable in any non-question begging way as far as I can tell.
Comment by DonaldM — September 13, 2006 @ 11:17 am
September 13th, 2006 at 11:25 am
Nick writes:
I just love the "only the creationists" are naive line. First off, no IDP that I know of is proposing "magical mircaculous" explanations. That you think so only betrays the absolute contempt you have for those who dare question the efficacy of Darwinian story. Yes, a full lab demonstration would be desirable, but, likely unrealistic, as you point out. But what is missing in the Darwinian explanation is any reason to believe that chance and necessity, or their combination have the capability to produce IC systems in the first place. Providing lists of homologous protein structures, or oranisimal similariiteis, which is all I've seen you do, Nick, doesn't tell us a thing about how Darwinian processes produced the systems in any non-question begging way. Or are we just supposed to accept the Darwinian thesis uncritically?
Comment by DonaldM — September 13, 2006 @ 11:25 am
September 13th, 2006 at 2:18 pm
Sure, the demand to see the flagellum evolve in a lab is unrealistic. But let's not forget the equivalent demand from ID critics about meeting the designer.
Comment by Krauze — September 13, 2006 @ 2:18 pm
September 13th, 2006 at 3:49 pm
In another blog, we are discussing the various set of assumptions used in the Evolution/ID debate. Based on the exchanges here, I felt a similar discussion would help clarify our various positions. I purposely used a generic label for each set (SET_A, SET_B, SET_C and SET_D). Please feel free to word smith a set to a version you would agree with.
I am offering you the opportunaty to show that you are arguing a position rather than just arguing. For the record, my position is SET_A.
Who is up for the challenge?
Comment by Thought Provoker — September 13, 2006 @ 3:49 pm
September 13th, 2006 at 5:19 pm
DonaldM wrote:
If it were mere pointing, it would be, but it's not anything of the sort.
1) There are similarities between protein sequences that fit nested hierarchies, which is very strong evidence.
2) When the statistical significance of the sequence similarities is lost to random noise (about 25% identity), structural biologists still find basically identical structures that link protein families (not organisms) to each other. Moreover, those occupy only a tiny fraction of available "sequence space."
3) The same nested hierarchies are derived when scientists consider amino acid changes alone vs. when they consider silent nucleotide changes alone.
Donald, can YOU offer an ID hypothesis that explains ALL of those data?
That's unsurprising, given that you clearly haven't looked at the data.
If sequences couldn't be placed into a nested hierarchy, or protein vs. nucleotide vs. silent nucleotide comparisons didn't give the same hierarchy when analyzed independently, the hypothesis of common descent would be utterly trashed.
Explanation? Why not look at the actual experimental data, like the experimental evolution of protein-protein binding from random starting sequences, using only chance and mecessity (aka selection)?
Krauze wrote:
Who, exactly, has issued such a demand?
P.S. Your polemic strategy of negatively labeling people who actually produce data as mere "critics" while you produce no data yourself (only criticism) is pretty slick, though.
Comment by Smokey — September 13, 2006 @ 5:19 pm
September 13th, 2006 at 6:01 pm
Smokey writes:
Hardly. Like every other piece of disconfirming evidence faced by evolution, we would see all sorts of hypothesis and speculations to fit, I mean force, the data into the evolutionary scheme.
And why would any of these be surprising under a scheme of common design? Or are these the results we would expect if and only if they were the result of common ancestry? Why the one and not the other? I don't find any of this data surprising. It is exactly what I would expect under an hypothesis of common design.
I notice that the nuts and bolts that hold my car together are quite similar to the ones used to hold my grandfather's John Deere tractor together. Yet for all those similarities, both my car and tractor are the result of common designs.
All of this to say that you are sneaking a metaphysical assumption into the equation. It's a version of the "god wouldn't do it this way" argument. What's missing is a way for science to determine that these observations could only be the case if and only if they were the result of common ancestry. That science has no way to do that makes the evidences you mention look pretty weak.
Comment by DonaldM — September 13, 2006 @ 6:01 pm
September 13th, 2006 at 6:48 pm
Hi Smokey,
"Who, exactly, has issued such a demand?"
There's a couple of examples here.
Do you agree that this demand is unrealistic?
"P.S. Your polemic strategy of negatively labeling people who actually produce data as mere "critics" while you produce no data yourself (only criticism) is pretty slick, though."
The term "ID critic" is used by most people on both sides of the "fence". Talkdesign.org, for example, writes: "Talkdesign.org is run by several volunteers, of a variety of religious and philosophical persuasions, who are all critics of ID and supporters of mainstream evolutionary biology."
BTW, in all the time I have discussed intelligent design, I have only met one other critic who objected to being called a "critic". Are you "myosin"
Comment by Krauze — September 13, 2006 @ 6:48 pm
September 13th, 2006 at 6:58 pm
DonaldM wrote…
So Donald, do you have a position or are you just arguing to argue? If you have a position, what is it? Are you making a positive hypotheses about how a designer (God?) would do things (see SET_B or SET_C of my previous post) or are you a Monday Morning Quarterback complaining that the Evolutionary Biologists are just doing it wrong or, worse, wasting their time?
Comment by Thought Provoker — September 13, 2006 @ 6:58 pm
September 13th, 2006 at 7:25 pm
Krauze wrote…
"Sure, the demand to see the flagellum evolve in a lab is unrealistic. But let's not forget the equivalent demand from ID critics about meeting the designer."
Smokey asked…
"Who, exactly, has issued such a demand?"
Krauze replied…
There's a couple of examples here.
The link Krauze supplied had this in the opening description…
Excuse me for butting in, but this directly ties into my set-of-assumptions post. Who is trying to convince whom of what? It isn't a demand when aswering the question "what would it take to convince you?"
Comment by Thought Provoker — September 13, 2006 @ 7:25 pm
September 13th, 2006 at 8:27 pm
TP writes:
Neither. I"m pointing out that the claims that evolutionary biologists make regarding the supposed evolution of IC biological systems aren't as well supported by the evidence as advertised, especially when the metaphysical blinders are removed.
Comment by DonaldM — September 13, 2006 @ 8:27 pm
September 13th, 2006 at 9:19 pm
DonaldM wrote…
Please excuse my colorful "Monday Morning Quarterback" remark, but I really don't see how you can deny that what you are doing is critiquing the efforts and work-product of Evolutionary Biologists. You need more than metaphysical blinders to avoid seeing that.
It's an American past-time. Telling others how they can do their job better. So, let me tell you how you can improve your side's credibility
It really would help if you provided at least a basic outline of your position. I earnestly tried to help you with my previous post (see SET_B). Without a stated position, you give the appearance that you are offering no alternative and nothing will ever be good enough.
Comment by Thought Provoker — September 13, 2006 @ 9:19 pm
September 13th, 2006 at 10:27 pm
Please excuse my colorful "Monday Morning Quarterback" remark, but I really don't see how you can deny that what you are doing is critiquing the efforts and work-product of Evolutionary Biologists.
Nonsense. Donald is critiquing that interpretation of that data which to a great degree is done by non-evolutionary biologists.
Comment by Bradford — September 13, 2006 @ 10:27 pm
September 13th, 2006 at 10:51 pm
I wrote…
Please excuse my colorful "Monday Morning Quarterback" remark, but I really don't see how you can deny that what you are doing is critiquing the efforts and work-product of Evolutionary Biologists.
Bradford Interjected…
This is a good start towards establishing common ground. It looks like our small group here can agree that, at the core, Evolutionary Biologists have been performing good science.
I also think there is agreement that outside forces are using and abusing the work-product of these earnest scientists for political and/or financial gain.
Now that we have cleared the air, we can focus on the issue of what we (not others) believe and test the validity of those beliefs. I have spelled out what I believe (see SET_A of my previous post). What do you believe?
Comment by Thought Provoker — September 13, 2006 @ 10:51 pm
September 13th, 2006 at 11:11 pm
Are you running for office or making money from this?
Comment by Bradford — September 13, 2006 @ 11:11 pm
September 13th, 2006 at 11:37 pm
DonaldM wrote:
In fact, ALL of them would be, particularly the ability to construct the same nested hierarchy from silent (i.e., nonfunctional) substitutions as you can from functional substitutions. In brief, they would all 3 be surprising because NO set of designed objects can be placed into a single nested hierarchy that can then be superimposed onto the nested hierarchy descibing the similarities of their components.
If you're having trouble with the concept of "nested hierarchy," would you like an example, or are you just going to bluster through?
They are not the results obtained from any sets of objects known to be designed, so unless you are willing to add some really wierd characteristics to your hypothetical designer, yes.
You haven't examined any data, Donald; you don't even understand the important concept of nested hierarchy that describes the data.
Really? Then go right ahead and name a set of designed objects that fit into only a SINGLE nested hierarchy that can be superimposed onto the nested hierarchy into which ALL of their components fit.
I dare ya.
That's nice, but you're missing the point by a mile. The relationships between those nuts and bolts cannot be described as a nested hierarchy. Do you know what "nested" means, Donald? "Hierarchy"
No, since you don't understand the concept of nested hierarchy, you're totally wrong about everything.
Not at all. It's a clear, absolute prediction of common descent. You're the armchair critic here who can't be bothered to look at the evidence, which along with the tools to analyze it, has been available to the public for years.
That's not how science works.
You're simply being dishonest if you claim that the evidence looks weak without ever looking at the evidence.
Krause wrote:
I see neither demands nor anything that suggests a meeting. Do you?
Yes, but you have yet to offer any evidence that such a demand has ever been made.
So what? It's still a slick polemic move when used by people who don't produce a single datum themselves. It's downright Rovian.
DonaldM wrote:
Huh? You've never looked at any evidence, and you're trying to make a patently false claim that groups of human-designed objects fit in single nested hierarchies along with their components.
Comment by Smokey — September 13, 2006 @ 11:37 pm
September 13th, 2006 at 11:44 pm
Bradford, if Donald thinks that human-designed objects and their components can each be placed into single, superimposable nested hierarchies, he's in no position to critique anything.
As for the latter part of your sentence, if you are claiming that the critiquing of sequence hierarchies is done by non-evolutionary biologists, you'd be spectacularly wrong. The vast majority of the sequence data has been produced by molecular geneticists, who, back in the more descriptive phases about a decade ago, often included evolutionary trees (nested hierarchies) in their papers describing newly-discovered genes. You see, that's one of the ways in which the molecular geneticists use MET to construct hypotheses about gene and protein function.
Comment by Smokey — September 13, 2006 @ 11:44 pm
September 14th, 2006 at 12:30 am
That was not my claim. I was pointing out that inferences, beyond critiquing of sequence hierachies, are made by individuals who are not evolutionary biologists.
Comment by Bradford — September 14, 2006 @ 12:30 am
September 14th, 2006 at 12:33 am
Is this a reference to what follows?
Comment by Bradford — September 14, 2006 @ 12:33 am
September 14th, 2006 at 3:37 am
Hi Smokey,
You missed a question: Are you "myosin"
Comment by Krauze — September 14, 2006 @ 3:37 am
September 14th, 2006 at 8:40 am
Explain why the Markov property and an intelligent generation and separation of (in von Neumann terms) a cellular automaton from its descriptor, are incompatible. If they are not incompatible then how do nested hierarchies exclude an intelligent inference?
Comment by Bradford — September 14, 2006 @ 8:40 am
September 14th, 2006 at 9:34 am
Hi DonaldM,
Donald, whats missing from your understanding is that arguing that "god can do it any way he wants to" isn't science. Of course any set of data is consistent with an omnipotent designer. Thats why an omnipotent designer isn't a scientific argument; its unfalsifiable. Evolutionary theory, otoh, is falsifiable because there could be data inconsistent with it; if, for example, every organism was utterly unique.
Oh, yeah, you already addressed this by making a grand, vague claim without any factual specifics supporting it. Care to give specific examples of evidence which falsifies evolutionary theory which has been "forced" into the evolutionary scheme?
Comment by Aagcobb — September 14, 2006 @ 9:34 am
September 14th, 2006 at 10:09 am
Smokey writes:
and
The concept of nested hierarchies (nh) just isn't all that difficult. At root it is an argument from homology. Perhaps you recall the name of Tim Berra and his book Evolution and the Myth of Creationism, in which he wrote:
This example became known as "Berra's Blunder" because he demonstrated that homology can be explained by either common decent or common design. The same is true of NH. The only reason NH becomes strong evidence for evolution is because of the additional metaphysical assumption that a designer wouldn't have done it that way.
The problem here is in specifying the mechanism by which these homologies would be the case if and only if they were the result of common ancestry. The best proposed mechanisms have been developmental pathways and genetic programs. But neither of these have been shown to account for homologies in the way needed by evolutionary theory. There really is no empirically demonstrated mechanism that explains homologies only as the result of common ancestry while at the same time eliminating common design. Based on actual evidence, including nh, it could be either.
Comment by DonaldM — September 14, 2006 @ 10:09 am
September 14th, 2006 at 10:14 am
Of course we know that every organism is not completely unique. But so what? That does not uniquely support an anti-ID position. In fact it is difficult to design complex entities without also having some shared similarities among the entities. More to the point though why would utter uniqueness to every varient be a feature unique to design? Any self-replication process implies shared features.
Comment by Bradford — September 14, 2006 @ 10:14 am
September 14th, 2006 at 10:21 am
aacobb:
Why would that falsify evolution? No one I know of has ever proposed a scientific reason why evolution would predict there be a universal genetic code? Why couldn't evolution work just as well with mulitiple codes? For that matter, no one has really offered a good Darwinian explanation for the genetic code itself. But either way, nothing about Darwinian evolution would demand, let alone predict that there would be a univeral code and not multiple codes. Your example betrays the implied metaphysical assumption that if God created the species, they would all be different and fixed (you recall, the "fixity of the species"). Scientifically, how do you know that?
I didn't use the word "falsify", I used the word "disconfirming"…they are not necessarily the same thing. Darwin expected the fossil record would eventually reveal this slow, step-by-Darwinian-step march of evolution. Instead, as Gould pointed out, the fossil record revealed stasis and extinction, with changes seemingly taking place over geologically short periods of time. This would seem to be disconfirming evidence for evolution…but, instead the hypothesis of puntuated equalibrium was born.
Whatever turns up, evolution can explain it.
Comment by DonaldM — September 14, 2006 @ 10:21 am
September 14th, 2006 at 10:33 am
No to the last question. There is no reason why multiple codes could not have developed but explaining any code based on stochastic chemical reactions is difficult enough.
Comment by Bradford — September 14, 2006 @ 10:33 am
September 14th, 2006 at 2:20 pm
Hi, DonaldM
Common descent would predict it, because organisms with utterly unique DNA could not share common ancestry.
You missed my point. Whether organisms are utterly unique or share common attributes, God can serve as an explanation. OTOH, utterly unique organisms cannot be explained by evolutionary theory.
False. Do you have any better examples than misrepresenting Darwin and Gould? You might want to research what legitimate scientific sources have to say about a subject before you rely on any more creationist propaganda.
Comment by Aagcobb — September 14, 2006 @ 2:20 pm
September 14th, 2006 at 2:34 pm
Bradford wrote…
No, my motivation is purely as a pastime activity.
I enjoy challenging (provoking) people to think about what they believe. In the process, I expand my knowledge and end up testing my own beliefs.
Bradford also wrote…
What is the ID position? More importantly, what is your position?
I wouldn't be surprised that people are tiring of my pressing this point but, seriously, arguing is just a waste of bandwidth without at least some understanding of each other's reference frame.
For example, I understand Behe's reference frame includes Common Descent. So, is arguing for Common Descent still an "anti-ID position"
It is easy to nit-pick a comprehensive set of assumptions that needs to accommodate all observed phenomenon. It is also practically meaningless unless you have a counter proposal. Even a "I agree with everything but this…" is a counter proposal.
So, I am asking you to think about what you do and don't accept about the current position I am restating here. Of the parts you don't accept, what are your alternatives?
My primary focus is to get you to think and question yourself. However, it would be appreciated if you share your thoughts so we all can discuss this topic intelligently.
Though Provoker's position statement…
Comment by Thought Provoker — September 14, 2006 @ 2:34 pm
September 14th, 2006 at 3:29 pm
Shared design features are also consistent with ID. What you need is evidence that is unique to your POV. Millions of different encoding conventions is no more an indicator of design than is a shared convention.
Comment by Bradford — September 14, 2006 @ 3:29 pm