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
September 14th, 2006 at 3:40 pm
Excuse me, but I just couldn't resist…
Bradford wrote…
Have you advised yourself that lately? What evidence is unique to your Point of View? An even better question is, what is your point of view?
Comment by Thought Provoker — September 14, 2006 @ 3:40 pm
September 14th, 2006 at 3:46 pm
Hi Bradford,
I know that Bradford; didn't I just say that? Anything and everything is consistent with ID; there is no evidence which is unique to evolution and inconsistent with ID. Thats why ID isn't science; since it can explain anything, in the end it explains nothing. What you and DonaldM don't understand is that evolutionary theory isn't measured by explaining something which can't be explained by ID. Evolutionary theory is measured by its ability to make testable predictions which allow for the possibility that the theory is wrong. There are a lot of possible versions of reality which could exist which couldn't be explained by evolutionary theory; there is no version of reality which can't be explained by an omnipotent designer.
Comment by Aagcobb — September 14, 2006 @ 3:46 pm
September 14th, 2006 at 3:59 pm
Aagcobb wrote…
Well said Aagcobb.
Please excuse my butting into your conversation with Bradford earlier, but I was bored this afternoon and that "POV" opening was just too tempting of a target.
Do you have any comment on my position summary?
(other than it is incomplete)
Comment by Thought Provoker — September 14, 2006 @ 3:59 pm
September 14th, 2006 at 4:09 pm
Hi Thoughtprovoker,
Yes:
I'm assuming you left an additional number out there (millions, billions?), but otherwise, I don't have any quarrel with what you wrote.
Comment by Aagcobb — September 14, 2006 @ 4:09 pm
September 14th, 2006 at 4:24 pm
Not so. A means of generating an encoding convention and information storage system from a stochastic series of organic chemical reactions would be unique to naturalism.
Comment by Bradford — September 14, 2006 @ 4:24 pm
September 14th, 2006 at 4:25 pm
Aagcobb wrote…
Oh, did I fail to mention that I personally witnessed the event but I just can't remember if is was the summer of 4,597,565,447 BC or the fall of 4,597,565,446 BC.
Thank you, here is the revised version…
Comment by Thought Provoker — September 14, 2006 @ 4:25 pm
September 14th, 2006 at 4:59 pm
aacobb:
Perhaps not with each other, but nothing in evolutionary theory would prevent the possibility that there could be multiple lines of ancestry all evolving simultaneously. It just so happens that what we have is but one universal genetic code, but evolutionary theory neither requires that possibility nor predicts it. There could just easily have been 2 or 3 or 4, and each evolve its ancestral lines.
I didn't misrepresent anything. Eldrege and Gould devoloped the hypothesis of punk eek to explain data in the fossil record that didn't fit with accepted evolutionary theory, or what was thought to be predicted by evolutionary theory. The point to be appreciated here, though, is that evolutionary theory doesn't really predict what the mode and tempo of change needs to be to fit with the theory.
Let's grant for the moment that everything you say here is correct. How does that make evolutionary theory correct? In the context of this thread we're still stuck with the fact that there is no specified mechanism that adequately explains the homologies upon which the supposed evolutionary pathways rely. We're still looking for a detailed, testable (and potentially falsifiable) model for the evolution of an IC system. Homologous protein sequences, such as those outlined in the Matzke and Pallen article, no matter how detailed, don't tell us a thing about how a Darwinian process produced the system, because there is no proposed mechanism to explain the homologies that avoids making a question begging argument. That's the problem. At root it is saying similarities due to common ancestry are proof of common ancestry and, voila, we can explain the evolutionary origin of an IC system, such as a bacterial flagellum.
Comment by DonaldM — September 14, 2006 @ 4:59 pm
September 14th, 2006 at 5:03 pm
Bradford
Excellent point, Bradford.
Comment by DonaldM — September 14, 2006 @ 5:03 pm
September 14th, 2006 at 5:18 pm
HeeHee.
Sorry, hope I didn't sidetrack anything; just found this quote hilarious.
Comment by Doug — September 14, 2006 @ 5:18 pm
September 14th, 2006 at 6:12 pm
Common descent would predict it, because organisms with utterly unique DNA could not share common ancestry.
Excellent point. What would prevent evolution within multiple encoding lines? If MET is on target then there would be nothing but dogma standing in the way.
Comment by Bradford — September 14, 2006 @ 6:12 pm
September 14th, 2006 at 6:44 pm
Dogma. I love dogmas.
Comment by Douglas — September 14, 2006 @ 6:44 pm
September 14th, 2006 at 7:39 pm
Um, guys, sequence homology is a direct result of the well-understood process of gene duplication and sequence divergence. That's your explanation, and it has been the explanation for decades, long before any of the flagellum homologies were discovered. In fact, back in 1996 everyone criticizing Behe noted that this was the general explanation for sequence homology, even though such an argument had not yet been made for the flagellum.
If this wasn't an important point, then all of the ID guys wouldn't have highlighted their "30 unique proteins" claim in all their articles.
"Common design" is just "our miraculous designer might have done it to look like evolution, because he can do things however he wants." With such arguments one can prove that the universe was created with "appearance of age" 6,000 years ago, or last Thursday for that matter.
As we deliberately quoted Darwin in our article:
"What can be more curious than that the hand of a man, formed for grasping, that of a mole for digging, the leg of the horse, the paddle of the porpoise, and the wing of the bat, should all be constructed on the same pattern, and should include the same bones, in the same relative positions?… Nothing can be more hopeless than to attempt to explain this similarity of pattern in members of the same class, by utility or by the doctrine of final causes. The hopelessness of the attempt has been expressly admitted by Owen in his most interesting work on the 'Nature of Limbs.' On the ordinary view of the independent creation of each being, we can only say that so it is; that it has pleased the Creator to construct all the animals and plants in each great class on a uniform plan; but this is not a scientific explanation."
Until "common design" is something more than "so it is" and "it has pleased the Creator" to produce homology, then you haven't got squat in terms of an alternative explanation for homology, you just have empty feel-good verbiage.
Comment by Nick Matzke — September 14, 2006 @ 7:39 pm
September 14th, 2006 at 7:46 pm
As for testability of the flagellum evolution model…In 2003, I wrote:
And then in 2006 Pallen et al. discovered:
So to summarize: I made a successful, testable prediction based on evolution. Therefore you are wrong that evolutionary models are not testable.
Game, set, match.
Comment by Nick Matzke — September 14, 2006 @ 7:46 pm
September 14th, 2006 at 8:13 pm
Matzke
ANd until you can provide a mechanism that explains all these wonderful homologies without begging the question, you have no explanation at all.
Comment by DonaldM — September 14, 2006 @ 8:13 pm
September 14th, 2006 at 8:17 pm
No, Nick, all you've done is assume evolution to prove evolution. No one is questioning that homologies exist. What you don't have is the mechanism to explain it. Unless you think that saying homologies due to common ancestry predict common ancestry is a testable prediction.
Looks like were back to love, to continue the tennis analogy!
Comment by DonaldM — September 14, 2006 @ 8:17 pm
September 14th, 2006 at 9:06 pm
One of the reasons critics of ID are easiliy refuted is because they attempt to shut off all possible intelligent inferences with data that is applicable only to limited conditions. Assume for the sake of argument that everything Nick has written about sequence homology is accurate including his flagellar inferences. There are still two types of ID inferences not addressed by his arguments. He has not countered Mike Gene's front loading or the origin of life scenario. If intelligence is a causal factor, at a point in time preceeding gene duplications within functional genomes of replicating organisms, then Nick's homologies are fruits of a design tree.
Comment by Bradford — September 14, 2006 @ 9:06 pm
September 14th, 2006 at 9:07 pm
Good. So what would be the point of your pointing that out?
Yes. There's nothing nested or unique about the hierarchies in which designed objects can be placed, and there's nothing superimposable about those derived from complex designed objects and their components.
Nested hierarchies exclude an intelligent inference because NO sets of designed objects can be placed in to a single, nested hierarchy that can be superimposed onto single, nested hierarchies representing the relationships between their shared components.
1) Are you aware of the distinction between homologous and orthologous genes?
2) Are you aware that MET predicts that as discrepancies and errors are resolved, that new data point to only a single nested hierarchy for groups of organisms as well as the sequences of the proteins and genes that they contain?
If so, please identify a group of designed objects that meet these criteria.
If it isn't difficult for you to understand, why are you pretending that tractors and their component nuts and bolts can be placed into nested hierarchies that can be superimposed upon each other?
Nested hierarchies? No. You're conflating a concept that you don't understand with an argument that you don't understand, while pretending to have examined evidence that you haven't seen.
No, sorry, I read the primary literature–that stuff that presents the actual evidence.
But Donald, Corvettes can't be arranged in a nested hierarchy that is superimposable on the nested hierarchy independently derived from the homologies between their components. It's merely an analogy that demonstrates a concept. It breaks down completely when applied to the components of those Corvettes. Do you agree, or disagree?
For example, weren't many of the components of those Corvettes not changed at all from year to year? How can one build nested hierarchies of homologies from identical objects?
It only was called that by people who lacked the intellectual sophistication (and/or honesty) to distinguish between analogy and argument. I find your attempt to try and write off independently-derived, superimposable nested hierarchies as mere homology to be as dishonest as your claims of familiarity with the evidence.
No, it's quite different, and you clearly aren't coming close to addressing the superimposition of the NH from organisms upon the NHs independently derived from their component protein and gene sequences.
Pardon me, but doesn't the whole notion of ID flow from the idea that living things LOOK designed (only tenable when one cherrypicks and avoids any depth of evidence)? IOW, that a designer WOULD have done it that way?
And aren't these superimposable NHs an absolute requirement if common descent is true? If we didn't see them, how could we possibly conclude that common descent is correct?
Sorry, but I've never heard anyone propose anything of the sort. But I guess that since you'll fabricate claims of familiarity with the evidence, you'll fabricate proposals from other people, right?
Sure there is. The ability to superimpose the NH of organisms on the NH derived from their components. That's not a characteristic of ANY group of designed objects. Unless you'd care to demonstrate that all the components of those Corvettes fit the same NH as the complete cars? Are you absolutely sure that GM didn't change bolt suppliers in the middle of a model year, so that nonfunctional differences (like numbers stamped on bolt heads) would be identical between late '53 and early '54 Corvettes, but different from early '53s?
Well, as it's been pointed out to you, ID by an omnipotent being is compatible with anything, so it predicts nothing, which makes it nonscientific.
Yes, but I'm not referring to mere "shared similarities." I'm referring to the construction of nested hierarchies from them, and when one does so with the complex entities and their components independently, one ends up with superimposable nested hierarchies.
Has anyone EVER designed complex entities for which those characteristics hold true?
Comment by Smokey — September 14, 2006 @ 9:07 pm
September 14th, 2006 at 9:38 pm
I post…
"Oh, did I fail to mention that I personally witnessed the event but I just can't remember if is was the summer of 4,597,565,447 BC or the fall of 4,597,565,446 BC."
To which doug reacted with…
I am glad you liked it and thank you for posting.
You didn't sidetrack anything. It looks like others are steadfastly protecting their undisclosed point of views.
If I read between the lines correctly, you seemed to be somewhat knowledgable of Behe's position. Am I correct that Behe accepts Common Descent as a valid scientific assumption? Do you share his opinion on that?
Comment by Thought Provoker — September 14, 2006 @ 9:38 pm
September 14th, 2006 at 10:16 pm
Nested hierarchies exclude an intelligent inference because NO sets of designed objects can be placed in to a single, nested hierarchy that can be superimposed onto single, nested hierarchies representing the relationships between their shared components.
My design candidate is the first cell from which all organisms are said to have descended. You did not answer my question. How do nested hierarchies satisfy the preconditions required to initiate a stochastic chain of events?
Comment by Bradford — September 14, 2006 @ 10:16 pm
September 14th, 2006 at 10:29 pm
Nick Matzke wrote…
DonaldM replied…
Gee Nick, all you did make a prediction assuming a hypothesis that to turned out to be true. What kind of "science" is that?!?
(for those who can't tell, that was sarcasm)
Honestly Nick, I do not see how you can deal with this as well as you do. It is obvious they know they know they will lose any rigorous comparison between their position (what ever it is) and yours. Taking pot shots is easy. Here, let me give it a try…
Sure, you identified the bulk of homologs for the Flagellum but you failed for two critical proteins. These missing links show the possibility that a very-powerful-but-not-quite-supernatural designer was involved. Until you eliminate this possibility, yours is a "just so" story. Oh, and by the way, if you somehow manage to eliminate the possibilty of this designer, he has a brother. You probably heard of him, he is kind of well-known.
(ironicly, I have to point out the above is not my true feelings)
Comment by Thought Provoker — September 14, 2006 @ 10:29 pm
September 14th, 2006 at 10:41 pm
Why would we need to assume anything about inferences? Why wouldn't we just note, for the sake of argument, that his prediction was clearly correct? Isn't prediction the scientific gold standard?
Bradford, you're confused. It's not up to Nick to address the arguments of others.
Why would he need to? And wasn't that Krauze's front loading anyway?
Then there would need to be some evidence predicted by such a front-loaded design, like being able to trace modern genes back to ancestral ones with no discernible function. If the ancestral ones have functions, then it doesn't meet any usable definition of front-loading.
Since you'll ignore that, let me make it more simple: if multicellular organisms, with all their intercellular functions, evolved from front-loaded unicellular organisms, we should find evidence of front-loading for intercellular functions (other than mating) in the genomes of those unicellular organisms.
Mike Gene wrote that she/he was too busy to look for that evidence, and that says it all.
Are you too busy too?
Why couldn't all organisms be descended from something that didn't meet the definition of a cell?
Sure I did. You just didn't like my answer.
Nice straw man!
In reality, the ability to SUPERIMPOSE INDEPENDENTLY-DERIVED nested hierarchies derived from whole organisms, functional changes in protein and DNA sequences, as well as the far more frequent but functionally silent changes in protein and DNA sequences, is required if common descent is correct.
Can you explain why, in none of your arguments, neither you nor Donald address this essential feature of superimposability?
Comment by Smokey — September 14, 2006 @ 10:41 pm
September 14th, 2006 at 11:14 pm
If histone H1 has no function in Tetrahymena then there would be evidence of front loading and you could become an ID evolutionist right?
My design candidate is the first cell from which all organisms are said to have descended.
Why couldn't all organisms be descended from something that didn't meet the definition of a cell?
Such as an intelligent designer.
How do nested hierarchies satisfy the preconditions required to initiate a stochastic chain of events?
Nice straw man!
No, this goes to the point of all your arguments. I've said before that my inference is made at the point of origin. If intelligence is the best explanation for life's origins and nested hierarchies the best evidence for what subsequently occured then would you want to push for descent by design? It has a good sound to it.
Comment by Bradford — September 14, 2006 @ 11:14 pm
September 15th, 2006 at 12:50 am
How would you demonstrate that a protein has no function? Wouldn't concluding a global negative require several more orders of magnitude of evidence?
And why are you disregarding the intercellular/intracellular distinction?
No, such as self-replicating, catalytic RNA.
They are predictions of a stochastic variation coupled with nonstochastic selection. Why are you using the straw man that MET is random, when selection is anything but random? Why are you having so much trouble with this idea of prediction? Do you have another way of doing science that doesn't involve testing predictions from hypotheses? If so, would you mind applying it to something like drug development, to demonstrate its superiority to those of us who hypothesize and test?
I keep making the point that these hierarchies are superimposable, and you haven't addressed that point at all.
That's nice, but unless you make predictions, it's scientifically worthless.
Because it doesn't explain why the hierarchies are superimposable. Why does having a "good sound to it" count for more than ability to make predictions?
Comment by Smokey — September 15, 2006 @ 12:50 am
September 15th, 2006 at 8:38 am
Bradford wrote…
This is quite a good start at articulating a position. It also helps explain the difficulties in communications between Bradford and Smokey, they were arguing about things they agreed upon.
If I understand correctly, the following is close to Bradford's position…
Comment by Thought Provoker — September 15, 2006 @ 8:38 am
September 15th, 2006 at 9:03 am
DonaldM wrote
True, but then each organism wouldn't be utterly unique, there would be other organisms it was related to, and one would be able to develop twin nested heirarchies for each set of related organisms. If each and every organism on earth was utterly unique, that would be inconsistent with evolutionary theory, except in the very beginning.
Comment by Aagcobb — September 15, 2006 @ 9:03 am
September 15th, 2006 at 3:27 pm
I'm not disregarding anything but am leaving possibilities open. The conditional attached to the H1 means further testing is in order.
Such as an intelligent designer.
No, such as self-replicating, catalytic RNA.
About which no data exists indicating why natural selection would act to influence an evolutionary process in the direction of a cell or even act at all.
How do nested hierarchies satisfy the preconditions required to initiate a stochastic chain of events?
They are predictions of a stochastic variation coupled with nonstochastic selection. Why are you using the straw man that MET is random, when selection is anything but random? Why are you having so much trouble with this idea of prediction? Do you have another way of doing science that doesn't involve testing predictions from hypotheses? If so, would you mind applying it to something like drug development, to demonstrate its superiority to those of us who hypothesize and test?
The purpose of the question was to point out that the predictions do not extend to initial conditions where a nonstochastic selection process has yet to be demonstrated. There is no selective value to any particular RNA sequence in an RNA world environment.
If intelligence is the best explanation for life's origins and nested hierarchies the best evidence for what subsequently occured then would you want to push for descent by design? It has a good sound to it.
Because it doesn't explain why the hierarchies are superimposable.
It doesn't have to. Once von Neuman requirements for self-replication are in place, variation in allele frequency can proceed. You can design a machine and then run it. You do not have to continually design to keep it running. The capacity for continuous function and adaptation already exist.
Why does having a "good sound to it" count for more than ability to make predictions?
I've suggested a prediction. 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, encoding RNA and proteins required by such mechanisms, genomes decay and become non-functional. The catalytic RNA envisioned as the replicating starter of the RNA world, entails sequence specificity enabling its catalytic properties. The RNA world proposes that copying mistakes are the raw material for change in the direction of a cell. The ID counter hypothesis is that nucleotide sequence changes would disable the only RNA world function- catalysis. Without ed&r mechanisms decay outpaces information gains; which themselves are dependent on an already existing encoding convention.
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. Ed&r genes are not generated without a natural selection basis.
When replication fidelity is 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.
A corollary is added to your superimposition capacity requirement. In prebiotic conditions the capacity of a stochastic process to generate and maintain nucleotide sequence patterns, independently identified as conferring functional utility, is required if common descent is correct. Two related predictions are:
1. Maintaining a sequence having functional utility requires multiple, interacting parts.
2. In the absence of pre-existing ed&r mechanisms, consisting of multiple interacting parts, the required invariance needed to maintain a useful function will be lost.
Tests would entail identifying nucleic acid sequence patterns conferring both resistence and tendency toward variance; identifying repetitive patterns affecting variation tendencies; and noting the frequency and distribution of any sequences influencing acceleration of genomic decay.
Comment by Bradford — September 15, 2006 @ 3:27 pm
September 15th, 2006 at 3:49 pm
Smokey
Really? Apparently it is a characterstic of biological systems. Unless you have independant evidence that biological systems are not designed, then your argument here is mere question begging. Whether or not biological systems are designed is part of the issue. So you're claim that superimposable NH's are not a characteristic of any group of designed objects already assumes that biological systems are not designed. If biological systems are, in fact, designed, as many think is the case, then your claim that no group of designed objects would have the characteristic of superimposable NH's is clearly false.
I'm not questioning the existence of superimposable NH's. Nor am I questioning the methods used to derive them. What I am questioning is the interpretation that this characteristic could only be the result of common ancestry, but not common design.
Comment by DonaldM — September 15, 2006 @ 3:49 pm
September 15th, 2006 at 4:28 pm
DonaldM wrote
I know this post goes way back up the thread, but I couldn't resist showing that Behe himself has demonstrated that point mutations have the capability of producing IC systems, as discussed here.
Comment by Aagcobb — September 15, 2006 @ 4:28 pm
September 15th, 2006 at 6:54 pm
But you aren't going to be testing anything. Besides, you weren't "leaving possiblities open," you asked, "If histone H1 has no function in Tetrahymena then there would be evidence of front loading and you could become an ID evolutionist right?"
Your idea that a single piece of negative evidence might be convincing is preposterous, but I guess when you have no data at all, even a single datum looks huge.
I wrote: "No, such as self-replicating, catalytic RNA."
We have replication and we have variation. What more would we need?
Bradford, predictions cannot possibly made about events in the past. They can only be made about events in the future, including the discovery of evidence from events in the past.
Where?
Not a prediction.
Not a prediction.
How can you have a related prediction when you have made no predictions? Aren't HeLa cells evidence contradicting your assertion (not a prediction) above?
A catalytic, self-replicating RNA avoids all of those problems.
But what you're missing here–by a country mile–is that both catalytic RNAs and proteins are not as constrained as you claim they are. As I've asked you before about proteins, what's your PREDICTION if I radically change the size of a conserved residue (from one of the largest to the smallest) in an active site, by substituting a residue not found in nature?
(the protein family is huge, BTW, so the negative finding is highly significant)
But that depends on aggressive ignorance about the notion of specificity, which you clearly have in spades.
So when scientists start with a completely random sequence and use error-prone PCR and selection to reevolve a specific protein-binding sequence, you would predict that they'd fail miserably, right?
That's a general assertion, not a prediction.
So what happens in immortalized cell lines?
Description, not prediction.
Description, not prediction.
Description, not prediction.
You flunk Grantsmanship 101. Here's how you make a prediction:
We hypothesize that mechanism V affects/controls W. This hypothesis predicts that if we do experiment X, we will observe result Y, and not result Z, which would falsify our hypothesis.
You see, Bradford, in this science game, hypotheses are tools, and those who shy away from testing them are ostracized. Those who claim an interest in a hypothesis, instead of interest in a phenomenon, will never have the courage or integrity to look for an experiment that has the potential to falsify their hypotheses.
Comment by Smokey — September 15, 2006 @ 6:54 pm
September 15th, 2006 at 8:50 pm
About which no data exists indicating why natural selection would act to influence an evolutionary process in the direction of a cell or even act at all.
We have replication and we have variation. What more would we need?
What experimental evidence do you have indicating that self-replicating, catalytic RNA replicates with varient descendent RNA?
Comment by Bradford — September 15, 2006 @ 8:50 pm
September 15th, 2006 at 10:24 pm
There is no experiment that could falsify abiogenesis. It takes no courage to conduct research in that field. Nothing is at risk whatever the outcome. I've repeatedly asked what is the selective basis for self-replicating RNA. The only answer I've ever received is varients that would replicate more efficiently. That does nothing to further the argument that a cell is at the causal end of this.
Comment by Bradford — September 15, 2006 @ 10:24 pm
September 16th, 2006 at 12:59 am
I was taking a look around Telic Thoughts and review this and other threads. On the slim chance that anyone cares, here are my observations…
Most of the threads seem topical. There are very few, if any, unreasonable personal attacks or attacks on other blogs. It looks like a fair mix of pro and anti ID posts (of course Pro ID is a little more dominent). All and all, it is obvious the blog keepers are doing a good job.
More observations…
This first thing I noticed was MikeGene's clear annunciations of his position. http://telicthoughts.com/?p=36...
Actually I saw that before my first post here. It was one of the things that impressed me about the site. Unfortunately, not everyone follows his example. I saw many arguments by ambush in this and other threads.
If looks like Bradford and Smokey have been going at this for a while now. I think they could just save time by posting both sides of the argument at one time. They should know them by heart now (can you say "Hstone Protein H1")
It took a little digging, but I am getting a feel for Bradford's position. He has some valid points. I look forward to going toe-to-toe with him if and when the time comes.
I am having difficulty understanding where DonaldM is coming from. I suspect going toe-to-toe with him will be quite ugly if and when that happens. Sometimes his logic processes can be… shall we say… interesting. For example…
Illion is apparently one of the been-here-forever guys. I would be interested to know if he stills stands by his initial assessment of me.
And then there is Doug. At least he has a sense of humor. From what little I have seen, he seems like a good guy (recommended promotion for Bradford).
I do want the thank you guys for the reception you gave me. It was I had hoped for (attacks from multiple sides). It was fun. If any, or all, of you want to continue the arguments or even to start another, I am up for it.
To Smokey, Aagcobb and, of course, Nick you guys seem to know your stuff (better than I) and are doing a good job arguing the evolution position.
To all, I have posted a far-out proposal in the open discussion thread. If you want a laugh, take a look at it. I will try to defend it against all comers (it is pro-ID, sort of).
Comment by Thought Provoker — September 16, 2006 @ 12:59 am
September 16th, 2006 at 1:21 pm
Of course not! Abiogenesis is a phenomenon, not a hypothesis. There are multiple hypotheses about how it could or could not occur that are testable.
And yet Tom Cech had the courage to test the hypothesis that proteins are required for catalysis by looking for catalytic RNA, and was rewarded with the Nobel Prize in Chemistry. You seem to have a problem with acknowledging his accomplishments, as you have this bizarre idea that proteins would be required for abiogenesis.
I'd say what Cech did was incredibly risky for his career.
I note that you lack the courage to make a prediction based on the assumption underlying your position–that catalytic RNAs and proteins can't tolerate sequence variation, which therefore constitutes an insurmountable barrier to abiogenesis.
I never provided that answer. The answer I provided was variation; the variation would vary catalytic efficiency, too.
You might want to reread what I wrote, Bradford. I explicitly argued that cellularity was not required at the beginning of abiogenesis, so your attempt to attribute "the argument that a cell is at the causal end of this" to me is ludicrous.
Comment by Smokey — September 16, 2006 @ 1:21 pm
September 16th, 2006 at 1:52 pm
Of course not! Abiogenesis is a phenomenon, not a hypothesis. There are multiple hypotheses about how it could or could not occur that are testable.
Tested with results that do nothing to confirm the idea.
It takes no courage to conduct research in that field.
And yet Tom Cech had the courage to test the hypothesis that proteins are required for catalysis by looking for catalytic RNA, and was rewarded with the Nobel Prize in Chemistry. You seem to have a problem with acknowledging his accomplishments,
You're full of it. He got the Nobel prize for his work and the intelligence behind it. It had nothing to do with courage and my comment was not aimed at him but nice try.
as you have this bizarre idea that proteins would be required for abiogenesis.
And Cech did nothing to prove otherwise. He did give ideologues like you something to hang your hopes on.
Nothing is at risk whatever the outcome.
I'd say what Cech did was incredibly risky for his career.
Baloney. If the results had turned out differently he would not have the Nobel prize and the plaudits but there was no risk to his career.
I note that you lack the courage to make a prediction based on the assumption underlying your position"“that catalytic RNAs and proteins can't tolerate sequence variation, which therefore constitutes an insurmountable barrier to abiogenesis.
I note you lack the integrity to note that my predictions have all been labled negative. The lack of tolerance for sequence variation, in the absence of error detection and control mechanisms, equates to a position that no minimal genome and hence no life can be generated without intelligent interference.
I've repeatedly asked what is the selective basis for self-replicating RNA. The only answer I've ever received is varients that would replicate more efficiently.
I never provided that answer. The answer I provided was variation; the variation would vary catalytic efficiency, too.
You are predicting the efficient and continuous repetition of short nonsense polynucleotides. That should advance civilization.
That does nothing to further the argument that a cell is at the causal end of this.
You might want to reread what I wrote, Bradford. I explicitly argued that cellularity was not required at the beginning of abiogenesis, so your attempt to attribute "the argument that a cell is at the causal end of this" to me is ludicrous.
Not nearly as ludicrous as your belief that catalytic RNA has significance if a cell is not at the causal end of a chain of events.
Comment by Bradford — September 16, 2006 @ 1:52 pm
September 17th, 2006 at 11:04 am
This thread would be a lot more user friendly if the discussion (including this request) not related to the flagellum and Nick's article could be exported to another thread or place.
Comment by Art — September 17, 2006 @ 11:04 am
September 17th, 2006 at 3:09 pm
Art, I agree.
The discovery of the existence of catalytic RNA does nothing to confirm or support the idea that life started with catalytic RNA?
He got the Nobel Prize because his work modified the Central Dogma of Biology. Nobels are given for impact, not intelligence.
Interesting. At the time of the discovery, Cech was an assistant professor who had a grant to find splicing enzymes, and he wasn't finding any among proteins. So according to you, people get grants renewed for failing, as well as tenure?
I noted that one of your attempted predictions was a negative, and you asked if I would be satisfied with a single datum. Did Stan Prusiner, whose prion hypothesis was negative (prions don't contain nucleic acids) ever ask any of his critics if they would be satisfied by a single negative demonstration?
The other things you claimed were predictions weren't predictions at all.
So where's my lack of integrity, Bradford?
Again, I note that you lack the courage to make a prediction based on the assumption underlying your position"“that catalytic RNAs and proteins can't tolerate sequence variation, which therefore constitutes an insurmountable barrier to abiogenesis.
What's your prediction if I radically change the size of a conserved residue (from one of the largest to the smallest) in an enzyme's active site, by substituting a residue not found in nature?
But the actual data show that there is an enormous tolerance for sequence variation among enzymes.
Real ribozymes suggest a relaxed error threshold.
Kun A, Santos M, Szathmary E.
The error threshold for replication, the critical copying fidelity below which the fittest genotype deterministically disappears, limits the length of the genome that can be maintained by selection. Primordial replication must have been error-prone, and so early replicators are thought to have been necessarily short. The error threshold also depends on the fitness landscape. In an RNA world, many neutral and compensatory mutations can raise the threshold, below which the functional phenotype, rather than a particular sequence, is still present. Here we show, on the basis of comparative analysis of two extensively mutagenized ribozymes, that with a copying fidelity of 0.999 per digit per replication the phenotypic error threshold rises well above 7,000 nucleotides, which permits the selective maintenance of a functionally rich riboorganism with a genome of more than 100 different genes, the size of a tRNA. This requires an order of magnitude of improvement in the accuracy of in vitro-generated polymerase ribozymes. Incidentally, this genome size coincides with that estimated for a minimal cell achieved by top-down analysis, omitting the genes dealing with translation.
Those pesky scientists–always producing new data!
Yet the actual data show that we can start with nonsense sequences and using variation and selection, quickly evolve function, including enzymatic function.
Why, exactly, would that be ludicrous, and if it is, why would it be more ludicrous than your blatant misrepresentation of my position?
Comment by Smokey — September 17, 2006 @ 3:09 pm
September 17th, 2006 at 7:02 pm
TP writes:
I'm not really sure what your purpose is in trying to categorize the people who post here. If you have questions about my position, I'll be happy to answer them. I am a bit puzzled about the meaning of your post here, though. Why would having a discussion with me "get ugly" I try not to resort to ad hominem attacks and stick to arguments. You cite the example above as if there was something amiss with my logic. Well, if you think so, why not point out what you think the problem is? I think my logic is pretty straightforward. If on makes the claim, as Smokey did, that no designed objects can be placed intot NH's that are superimposable on each other, and cites biological systems as an example of that, as Smokey also does, it seems pretty straightforward to say that unless one has independant evidence that biological systems are not designed, using the example is begging the question. Where do you have a problem with that?
Comment by DonaldM — September 17, 2006 @ 7:02 pm
September 17th, 2006 at 7:07 pm
According to me Cech knew the demands and risks of his profession and operated within them just as surgeons know the risks of lawsuits, that come with errors and perceived errors, every time they head to the OR. Police officers know the risks inherent to their profession, as do soldiers with theirs and any worker in any occupation who must traverse through a crime ridden area, to and from work, knows the risks that go with that. If you want to label tens of millions of people as couragous, for going about their business, and think you have made anything other than a banal point, then go ahead.
I note you lack the integrity to note that my predictions have all been labled negative.
I noted that one of your attempted predictions was a negative, and you asked if I would be satisfied with a single datum. Did Stan Prusiner, whose prion hypothesis was negative (prions don't contain nucleic acids) ever ask any of his critics if they would be satisfied by a single negative demonstration?
Where did I claim a single demonstration was sufficient?
So where's my lack of integrity, Bradford?
Answer the previous question.
Again, I note that you lack the courage to make a prediction based on the assumption underlying your position"“that catalytic RNAs and proteins can't tolerate sequence variation, which therefore constitutes an insurmountable barrier to abiogenesis.
What's your prediction if I radically change the size of a conserved residue (from one of the largest to the smallest) in an enzyme's active site, by substituting a residue not found in nature?
If your enzyme operates within an OOL context then fill me in on how such enzymes were generated in the first place and what function they perform. If the context is cellular and ed&r mechanisms are not present, the prediction is the genome within which the relevant coding nucleotides are found, will lose information faster than a selection process can add it, resulting in genomic decay eventually disabling overall function.
The lack of tolerance for sequence variation, in the absence of error detection and control mechanisms, equates to a position that no minimal genome and hence no life can be generated without intelligent interference.
But the actual data show that there is an enormous tolerance for sequence variation among enzymes.
Real ribozymes suggest a relaxed error threshold.
Kun A, Santos M, Szathmary E.
The error threshold for replication, the critical copying fidelity below which the fittest genotype deterministically disappears, limits the length of the genome that can be maintained by selection. Primordial replication must have been error-prone, and so early replicators are thought to have been necessarily short. The error threshold also depends on the fitness landscape. In an RNA world, many neutral and compensatory mutations can raise the threshold, below which the functional phenotype, rather than a particular sequence, is still present. Here we show, on the basis of comparative analysis of two extensively mutagenized ribozymes, that with a copying fidelity of 0.999 per digit per replication the phenotypic error threshold rises well above 7,000 nucleotides, which permits the selective maintenance of a functionally rich riboorganism with a genome of more than 100 different genes, the size of a tRNA. This requires an order of magnitude of improvement in the accuracy of in vitro-generated polymerase ribozymes. Incidentally, this genome size coincides with that estimated for a minimal cell achieved by top-down analysis, omitting the genes dealing with translation.
Those pesky scientists"“always producing new data!
Indeed they are and more of it is needed to answer questions begged by your reference. If the assumption that a minimal genome of 100 different genes is a given then we are still without any information as to how the sequence specificity required by a small genome of this size was generated from initial conditions. Your allusion to self-replicating RNA provides no answers particularly when you avoid the issue of selectivity criteria.
You are predicting the efficient and continuous repetition of short nonsense polynucleotides. That should advance civilization.
Yet the actual data show that we can start with nonsense sequences and using variation and selection, quickly evolve function, including enzymatic function.
Efficient replication of nucleotide nonsense gives us more nonsense. You have yet to cite a reason why a random result, yielding a sequence with enzymatic properties, would be selected in the absence of a preexisting function involving a substrate and a biological mechanism.
Comment by Bradford — September 17, 2006 @ 7:07 pm
September 17th, 2006 at 11:43 pm
DonaldM wrote…
Thank you for responding.
I had multiple purposes for my post. One was that I have a short-lived, unique bit of knowledge. Someone's first impression of this blog and the people in it. I thought I would share that.
As far as cataloging positions, it comes from my years as a debator. Who is making affirmative arguments? Who is only making negative ones? Most newsgroups/blogs devolve into nothing but negative attacks. I have noticed it is even worse in the ID/Darwin wars. It is so bad that I felt compelled to present an affirmative proposal supporting ID in the open discussion thread. Thank you for your offer of answering my questions. Here are the basic ones…
What is your assumption for the age of the earth?
Was the earth's creation fundimentally due to natural forces?
Do you assume the earth was designed?
What is your assumption for when the first life appeared on the earth?
Do you believe everything derived from the first living organisms?
(as opposed to new "kinds" creation at various points in history)
What mechanisms do you accept as reasonable for explaining the diveristy of life on earth we see today?
I have provided my answers to these in my previous posts. If you have any questions for me, please feel free to ask.
DonaldM wrote…
I noted the general lack of ad hominem attacks. I also agree, you have been polite. I fear our discussion might get ugly because it is likely we both will get very frustrated. We will have to work very hard not to argue past each other.
Ok, I am taking a deep breath… in… out….
While I have problems with what you just said, I will explain my frustration with what you posted previously, which was…
Let's rewrite your statement using different nouns…
Whether or not Corvettes are boats is part of the issue. So you're claim that boats float already assumes that Corvettes are not boats. If Corvettes are, in fact, boats, as many think is the case, then your claim that boats float is clearly false.
It is late, so I will stop here. Thanks again for posting. I look forward to seeing your responses to my questions. May I suggest we just drop the logic puzzles before it gets "ugly".
Frankly, I am more interested in seeing how our concepts of evolution differ. It may very well be the case that we agree on more things than we disagree.
Comment by Thought Provoker — September 17, 2006 @ 11:43 pm
September 18th, 2006 at 12:25 pm
TP:
I am not a YEC. I have no problem with the earth being as old as geologists say it is, or the cosmos being as old as cosmologists and astro-physicists claim. Did the earth come into existence through "natural" forces or was it designed? Well, I don't know how to answer that one. I think the evidence of nature both on earth and in the cosmos is strongly in favor of the cosmos and everything in it being the result of deliberate, intelligent design. That would include earth, but doesn't necessarily mean that earth's production involved some miraculous act outside the laws of nature. It could be that the act of creation set up the conditions and laws, through which earth would come to be through a process working in concert with the laws that govern the cosmos. I have no real issue with that.
As for life on earth, I have serious doubts that evolution as commonly thought of in the ordinary way can account for all the diversity of life that we observe. I have several reasons for this. One is that biological systems seem to exhibit large amounts of complex, specified information not reducible to the simple laws of physics and chemistry operating through chance and necessity or their combination. Another is that many biological systems exhibit the feature of irreducible complexity, also not reducible to the simple laws of chemistry and physics operating through chance and necessity or their combination.
Based on what we have actually observed in biological systems, there does appear to be limits on adaptive change within organisms. Granted, I don't know of anyone who has adequately described in biological terms what the barrier to change might be, but is does seem to be the case. Might be a fruitful area for future research. I suspect that the more we know about DNA, the more evident such barriers to change might become,
but that's just a guess at this point.
As to the mechanism of diversity, I'm not entirely certain. No question that evolutionary changes due to the ability of organisms to adapt to environmental change have played a role. But as I alluded earlier, the extent of those adpative changes seem limited. And we really haven't observed much beyond adaptive change in biological systems. The mechanism a designer might have used to impart the necessary information into the biosophere might also be a fruitful area for future research. That has been the contention of Behe, Dembski and others in the ID camp.
What I don't doubt is that biological systems exhibit many feartures that in any other realm we would normally associate with design. The prohibition on design considerations seems to me to stem, not from scientific considerations, but philosophical ones, and that further those philosophical considerations are themselves not without serious problems.
Now, all of this is way beyond what this thread is about, but you asked.
Comment by DonaldM — September 18, 2006 @ 12:25 pm
September 18th, 2006 at 3:40 pm
No, I'd only label the subsets of people in those professions who make courageous decisions as courageous, not all of them. Cech risked his career. So do some, but clearly not all, surgeons, police officers, and soldiers. Many who take courageous risks lose their careers. Therefore, your statement about Cech was false.
I wrote: Did Stan Prusiner, whose prion hypothesis was negative (prions don't contain nucleic acids) ever ask any of his critics if they would be satisfied by a single negative demonstration?
Reread what I wrote above. You ASKED me if a single negative demonstration would be sufficient here:
"If histone H1 has no function in Tetrahymena then there would be evidence of front loading and you could become an ID evolutionist right?"
So where's my lack of integrity, Bradford?
Done. Where's my lack of integrity?
I asked: What's your prediction if I radically change the size of a conserved residue (from one of the largest to the smallest) in an enzyme's active site, by substituting a residue not found in nature?
Bradford, quit babbling talking points. My question is simple; the OOL context and the rest of the genome coding for this enzyme is irrelevant. Please quit bobbing and weaving and predict will happen to the activity of the enzyme. Here are 4 choices:
1) Activity will almost certainly be lost.
2) Activity will certainly be lost (your polemic assumption)
3) Activity will be retained.
4) The original activity will be retained, and the ability to hydrolyze a new, synthetic substrate is gained.
This is simply a direct prediction of your ludicrous assumption that enzymes can't tolerate sequence variation. I'm even stacking the deck for you by asking you to predict the results of a variation with 3 strikes against it: it is in the active site, contacting the substrate, the new residue is not found in nature in any member of this huge family, and it is the most radical size substitution possible.
Um, Bradford, you might try reading before attacking, as no one is making assumptions about minimal genome size.
I'm directly making selectivity criteria an issue, by noting that you continue to lack the intellectual courage to make a simple prediction as detailed above. You claim that enzymes can't tolerate variation, but you really don't have a clue about reality.
Error-prone replication of nucleotide nonsense, coupled with selection, gives us function. Would you like me to cite the best experimental example of this so that you can ignore it or quote-mine it?
Harvesting of energy that is put into self-replication, such as hydrolysis of high-energy bonds–as the protein about which you are afraid to predict does.
Comment by Smokey — September 18, 2006 @ 3:40 pm
September 18th, 2006 at 6:28 pm
Since I've indicated that cellular variation is a reality and my reference is an OOL scenario, the enzyme context means everything. You either are trolling or engaged in deliberate distortion.
Please quit bobbing and weaving and predict will happen to the activity of the enzyme. Here are 4 choices:
1) Activity will almost certainly be lost.
2) Activity will certainly be lost (your polemic assumption)
3) Activity will be retained.
4) The original activity will be retained, and the ability to hydrolyze a new, synthetic substrate is gained.
The prediction is simple. Enzymes, substrates and biological function do not arise (which includes a means of storing information and passing it to descendents) from a prebiotic starting point. Test this by with any genome, encoding the enzyme and its function but without ed&r coding capacity mechanisms. Genomic function related to the enzyme and all other biological functions will decay. Unchecked genomic decay does that. This would favor the conclusion that activity is neither lost or retained because it never would be generated in the first place. The genomic law of entropy reads: information loss exceeds gains without ed&r mechanisms in place at the outset.
Comment by Bradford — September 18, 2006 @ 6:28 pm
September 18th, 2006 at 8:53 pm
Along with a lot of stuff I didn't copy, DonaldM wrote…
I wouldn't mind at all if this conversation gets moved, but I do think it is still on topic. It deals with why the Pallen/Matzke paper is important.
In debates, the affirmative side proposes changes to the Status Quo. Nick's paper is an argument from the negative side saying the affirmative proposal is not needed. So…
What is being proposed?
More specifically, what is DonaldM proposing?
I didn't want to put words you your mouth, but I had to do some guessing. Therefore, please update this to your liking.
DonaldM's thinking…
I had to guess on the "1.5 billion years", do you think any new kinds were created after that? If so, do you have an opinion on when the last new kind was created?
I am not positive you accept natural selection as one of the processes for Environmental Adaption. It sounded like it, but I wasn't sure.
Thought Provoker's thinking…
I repeated my thinking here for comparison purposes. Please bear with me for one more round of posts. Don't worry about identifying what you don't believe or want the evidence shows. The purpose here is whether or not our thinking is consistant with itself.
The next step will be to see how the Pallen/Matzke does, or doesn't, effect our thinking.
Thank You for your cooperation and patience
Comment by Thought Provoker — September 18, 2006 @ 8:53 pm
September 18th, 2006 at 9:32 pm
Hi, Krause. You wrote:
I didn't find an answer to that. Actually, I like "Smokey" better. But I catch a faint whiff of brimstone whenever I see it. http://telicthoughts.com/wp-in...
Comment by Lutepisc — September 18, 2006 @ 9:32 pm
September 19th, 2006 at 5:41 pm
The reality of variation is not the issue we are debating. We are debating whether your global assumption that there is a "lack of tolerance for sequence variation" has any basis in reality.
Your evasions say it all.
The context here is both in vitro and in vivo. The in vitro condition is just a buffer with potassium, sodium, and magnesium salts, as well as the substrate.
How do you figure? Did you not claim:
"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."
There you are. I asked you about HeLa cells–have they lost "function enabled by specific nucleotide sequences" "in the absence of error detection and repair mechanisms"
Why didn't you respond?
If you're so sure that errors cause genomes to decay and nonfunctional, wouldn't you need to know something about the level of sequence specificity required to maintain function?
Then why isn't this followed by a simple prediction?
What does this have to do with a prediction? I'm simply asking you why you are afraid to apply your general assumption,
"The lack of tolerance for sequence variation…" to a specific case.
What is the real-world level of tolerance for sequence variation at the level of single proteins, Bradford? Do sequences not found in nature lack function? If I can make those three strikes against an enzyme, how can you assume that there is a general "lack of tolerance for sequence variation"
Comment by Smokey — September 19, 2006 @ 5:41 pm
November 16th, 2006 at 3:37 pm
Nick, is this available free online yet? I'm a pretty cheap guy
But I'd really like to read this.
Comment by Doug — November 16, 2006 @ 3:37 pm
September 20th, 2008 at 12:53 pm
[...] Since 2003, Matzke hooked up with Mark Pallen, a researcher who studies the flagellum/TTSS and who uncovered sequence evidence that indicated the flagellar gene FliH is a fusion of domains that are homologous to the b subunit and the delta subunit of the F-ATPase. This was a significant piece of support for Matzke’s hypothesis. And in 2006, Matzke and Palin published a paper in Nat Rev Microbiol.and I congratulated Nick. [...]
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