Talkorigins - on the reducible complexity of the flagella

They do this by means of any number of specialized protein secretory systems. One, known as the type III secretory system (TTSS), allows gram negative bacteria to translocate proteins directly into the cytoplasm of a host cell (Heuck 1998)....

At first glance, the existence of the TTSS, a nasty little device that allows bacteria to inject these toxins through the cell membranes of its unsuspecting hosts, would seem to have little to do with the flagellum. However, molecular studies of proteins in the TTSS have revealed a surprising fact – the proteins of the TTSS are directly homologous to the proteins in the basal portion of the bacterial flagellum.

link

I could certainly buy into the notion that there's a (probably non-teleological) genetic intelligence. It seems at least plausible that the universe was designed to support life, given that there's no other element that seems like it could effectively take the place of Carbon in biology. (Though that's very hard to prove and it's impossible to figure out what the alternate set of possible universes might look like.) But irreducible complexity arguments get shot down almost as quickly as they're thrown up. Eyes are not irreducibly complex. Flagella are not irreducibly complex. Life recycles its components relentlessly. How many times does this line of reasoning have to be stabbed before it dies?

Posted by: Ryan W. on July 9, 2009 08:49 PM

Next problem: Looking at Wikipedia, I note that homologous proteins are those [seemingly] derived from a common ancestor. Yet it seems Miller then uses these in a manner which necessarily implies he's talking about the exact same proteins as in the flagellum:

If the flagellum is indeed irreducibly complex, then removing just one part, let alone 10 or 15, should render what remains "by definition nonfunctional." Yet the TTSS is indeed fully-functional, even though it is missing most of the parts of the flagellum.

It seems what he's actually saying, if you read carefully, is that there are similar proteins in TTSS, and hoping, again, the reader won't notice the switch: "Look, this other non-engine thing has some parts which look (and perhaps behave) a bit like the other parts in that engine." Well, okay, interesting, but that's not the question now, is it?

He's not even satisfying his rather minimal straw man here: he says this was made by taking away parts from the flagellum. But that isn't so, it's done by taking away parts, and then also changing the ones that remain. (Or, more to the point, vise-versa, starting by mutating — perhaps very significantly — the smaller assembly in a way which would appear to "prepare" it for it's future as a rotor.) Naughty!

Again, perhaps another presenter could flesh out this or a similar argument in more detail, but it doesn't seem the case would sound as strong then. Instead, it looks very much, to me, like he's pulling several consecutive slights of hand and hoping the reader will skip over the pesky missing connections. Perhaps I should assume better, but the apparent presence of multiple such feints doesn't communicate intellectual honesty and seriousness to me.

He goes on to attack what seems to be a related argument from Dembski, but I think, given my own limited time and the apparent problems (putting it nicely) in his first argument, I think I'll choose not to bother, at least yet.

I decided to write the above response on my own, consulting no others, to see what I'd find — then look, when done to see how others responded.

Picking one off the Discovery site, there's this, which mentions the flaw I spotted (heh: using the same analogy I picked), and notes several others.

Behe and other ID-proponents have long-acknowledged "exaptation" or "co-option" as an attempt to evolve biological complexity, and have observed many problems with "co-option" explanations. [...] one could find a sub-part that could be useful outside of the final system, and yet the total system would still face many points along an "evolutionary pathway" where it could not remain functional along "numerous, successive, slight modifications" that would be necessary for its gradual evolution.

Again, I don't much like the IC argument for just this reason: if you quote a bit of it out of context, one can play various games. (Another is to show that something can still operate with one or two missing parts -- which actually DOES seem to follow from Behe's simplest phrasing, out of context. Yet if my car can operate without its radio and mudflaps, it doesn't show that the car, or some core representation of it isn't irreducibly complex.)

Miller also avoids talking about assembly pathways, viability along gradual mutations from his two functioning points*, etc, which are all issues raised by ID proponents. Again, he does seem to want to substitute stripped-down, significantly-altered arguments for the real debate which is going on.

(* Recall IC was a response to Darwin: a part would be produced from another by one viable mutation at a time. This is why the "removing one part" (at a time, per evolutionary step, or conversely, adding) aspect is important, and why just pointing to some small sub-assembly misses the point. Miller presents his alleged 10-15 part reduction (more really) as though it's much stronger than a 1-2 part reduction, when, in fact, it's much weaker — fatally so. A hubcap may roll off a car and function as a hillbilly salad bowl, but that doesn't mean we have an every-step-viable pathway from salad bowl to car.)

Behe's own response is here, and also notes:

The TTSS contains ten or so proteins that are homologous to proteins in the flagellum. The flagellum requires an additional thirty or forty proteins, which are unique.

And here's more on the alleged homology:

Add to this the fact that some of the homologues between the flagellar system and the TTSS system are not that homologous. The FliN in TTSS is only homologous to ~80 C-terminal residues of flagellar FliN (out of 137aa). There is very little FliG similarity and TTSS FliF is missing the C- and N-terminal domains that are involved in forming the MS ring. All that is left of FliF is about 90 out of over 550 amino acid residues. What this means is that the TTSS system cannot rotate. Evolving the ability to rotate would involve the addition of a sizable number of specifically sequenced residues.

There's more, but that's enough for the moment.

Look, I'll be totally frank here. I'm a bit of an agnostic on this particular question, and example. But what I find so darned interesting in these ID-related debates how often those attacking ID seem to be playing (out of ignorance or malice, it's hard to say) rather, shall we say, fast and loose. Is this another such case? Sure looks like it to me. Set me right if you think otherwise.

Great talking to you as always, Ryan!

Posted by: Tim (Random Observations) on July 10, 2009 12:32 AM

I agree that Miller puts a lot of padding in his article. I'd hoped to correct for this by including the relevant exerpt as my point was to indicate the similarity between the flagella and the TTSS, but I should have included a note explaining this as well. Here is an article that is, while not peer reviewed, more technically oriented and to the point. article

As I said above, in general, I don't think irreducible complexity (IC, today) is a particularly strong argument: it requires the one making it to (seemingly) prove a negative, and it also is hard to explain well (and easy to misstate) so that it's rather easy for people to think they're "disproving" it when they're not.... Yet if my car can operate without its radio and mudflaps, it doesn't show that the car, or some core representation of it isn't irreducibly complex.

I agree with your criticisms.

After taking the time to figure out how Behe actually defines "irreducible complexity" I can't recall a single person who invoked it that explained it the way that Behe does or managed to insert the necessary caveats that he does. So more than just being hard to explain or understand, it seems to be actively popularly abused by its proponents.

I wondered if Behe started with an overly strong assertion and tempered it or if he simply managed to confuse his entire listening audience. The vast majority of arguments that I've read on IC paraphrase Darwin's assertion; "If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. "

For instance;

Evolution cannot build irreducibly complex structures because evolution requires that biological structures arise in small steps, each of which allows for the structure to perform some function. For irreducibly complex organs, the organ is only functional if all parts are present. In this “all or nothing� game, intermediate stages of evolution are impossible because they would not function. (emphasis added) source

The repeated assertion is that irreducible complexity refutes Darwinian evolution.

After reading through your linked article from the Discovery Institute, it seems that this assertion comes from Behe's book "Darwin's Black Box"

Design theorist and biologist, Michael Behe, defines “irreducible complexity� by looking at a biological system to see if it can be produced in a step-by-step evolutionary fashion. Behe defines irreducible complexity in his book Darwin’s Black Box:

“In The Origin of Species Darwin stated:

'If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.'

A system which meets Darwin's criterion is one which exhibits irreducible complexity. By irreducible complexity I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning.�

(Michael Behe, Darwin's Black Box, pg. 39 (Free Press, 1996) (emphasis added).)

So Behe insinuated that IC was a possible refutation of Darwinian evolution.

But then he hedges; “Even if a system is irreducibly complex (and thus cannot have been produced directly), however, one can not definitively rule out the possibility of an indirect, circuitous route. As the complexity of an interacting system increases, though, the likelihood of such an indirect route drops precipitously. And as the number of unexplained, irreducibly complex biological systems increases, our confidence that Darwin’s criterion of failure has been met skyrockets toward the maximum that science allows.� (Michael Behe, Darwin’s Black Box, pg. 40.

But this second claim doesn't seem to follow. As long as you can change a system in a series of steps, whether one of the components is "irreducibly complex" is not at all relevant to Darwin's criteria or the probability of the system. A characteristic of evolved systems seems to be their fault tolerance. Humans, for example, have multiple copies of the gene for histones, which are spindles around which DNA strands are wrapped. We are also capable of withstanding many physiologically altering chemicals without actually dying. And it seems likely to me, though this is partly speculative, that certain portions of critical DNA are much more highly conserved than others, even prior to natural selection. On a similar note, there are cases where substance A would work and C, D, and E would also work, which confounds probability estimates (since the number of possible functional outcomes are not known, and are essentially unknowable, since the set of possible functions has not been determined. This touches only tangentially on your arguments, I realize.)

Used as a disproof of Darwinian evolution (which is the only way I've ever heard it used, with the recent exceptions of originator of the term (Behe) and Debinski). If the purpose of arguing for irreducible complexity is only to argue that precursors of flagella might not have functioned as flagella, then the argument may very well be true but not particularly novel or insightful, much less deserving of the attention that it has received. I've seen no good demonstration of the improbability of indirect evolution in complex systems, which is critical to using IC to disprove Darwinian evolution.

By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning. source cited only as a source for Behe's definition

Behe has conceded that “if a system is irreducibly complex (and thus cannot have been produced directly), however, one can not definitely rule out the possibility of an indirect, circuitous route� ...Thus, according to Behe, a more effective, more complex mousetrap evolving from a simpler version of itself would constitute direct evolution. A complex mousetrap evolving from a complex paperweight would constitute indirect evolution. Irreducible complexity is seen as a challenge to direct evolution. source

The issue for Darwinian evolution, however, is not that a car with wires removed can't drive, but whether it can perform any function whatsoever. The body of the car might make a suitable home, for instance, with the engine functioning as some form of heater.

The Discovery Institute, which you linked to, seems to flirt with this error; Natural selection purportedly builds complex systems from simpler structures by preserving a series of intermediates, each of which must perform some function. With the flagellar motor, most of the critical intermediate structures perform no function for selection to preserve.(emphasis added)

So while the Discovery institute is arguing for Intelligent Design rather than God it seems to abuse IC in the common fashion, by assuming that all evolution is what Behe terms "direct evolution."

Dembski does make the interesting argument that the TTSS may have evolved from the more complex flagelar apparatus (the prevailing mainstream belief seems to be that the two might have had a common ancestor), which I'll have to consider, and that may take some time. His arguments were several;

1)TTSS is encoded on plasmids, flagella typically are not, (despite being virulence factors.)

2)Flagellar components tend to be encoded on genes in different parts of the cell.

3)TTSS supposedly requires interaction with multicellular life.

4)Flagella have more complex apparatus than TTSS.

The first two arguments aren't particularly persuasive. Genes have been migrating from mitochondrion into their host genomes for eons. It's unclear to me to what degree modern microbes are, reliably, 'living fossils' of far more ancient microbes. The potential for germ line gene sharing is huge compared to multicellular life. It seems that the predominant view is that the TTSS and eukaryotic flagella had a common ancestor (not that the TTSS evolved from the flagella as the Discovery institute states.)

The final two, I'll have to consider a bit longer.

The more general form of the argument, however, that the flagella could have been formed from some type of secretory system, seems quite reasonable considering that the modern flagella contains a type of secretory system in it.

Posted by: Ryan W. on July 11, 2009 01:59 PM

I was also impressed with the article at the last link I'd used (which I found for searching on "Miller TTSS homologous" or something like that) -- should really take a look if you haven't. The author is engaging (and refuting, it seems to me) a much more sincere attempt at rebuttal than Miller's.

Also, I realized that IC was probably being misrepresented in the fashion Miller did quite often, given that you even thought perhaps that's was what Behe was arguing. Even if so, nothing I can say: I was also pretty much getting the arguments from opponents until recently. I've been guilty of this in a number of areas, and am still trying to grow out of it.

Thank you for all these things.

The most parsimonious explanation seems to me that there is some form of genetic intelligence, which I put forward and which I could support to some extent.... I realize I'm still in the minority, here.

I'm very interested in hearing more on this subject — feel free to email me more if you'd like, perhaps I can even post it here. As you well know, I also hold quite a number of "minority" opinions, and am no longer as swayed by consensus as I used to be. (Seeing the number of patently wrong things which were or still are held by the majority of those who really ought to know better...) That said, I'm going to skip over that, for now, since I have limited time and focus at the moment.

So more than just being hard to explain or understand, it seems to be actively popularly abused by its proponents.

Agreed, sadly. Upon finding, after writing all the above, that Miller had actually testified in court several times on the matter (and knowing that these specific rebuttals had been popularized also) I found it very hard to believe that Miller was simply naive regarding what Behe was actually saying. So I have come to suspect Miller is, to put it bluntly, actually being dishonest at some level. He's both too smart and too actively involved, it seems to me, to not at least understand what is actually meant.

(In contrast, I would currently credit Matzke (last link above), arguing a similar position, with complete honesty and sincerity.)

I wondered if Behe started with an overly strong assertion and tempered it or if he simply managed to confuse his entire listening audience.

I would guess that certainly there's been "learning" all around, including perhaps clarifications or even evolution of Behe's own position to meet objections and misunderstandings. BUT, that said, I would suspect not significantly so. My understanding is that Behe started out as an atheist Darwinist, so I doubt he would have then come out, full blown, with the sort of over-the-top formulation his critics usually want to use instead of his own. (I'd have to read Black Box to find out.)

As long as you can change a system in a series of steps, whether one of the components is "irreducibly complex" is not at all relevant to Darwin's criteria or the probability of the system.

I think you're treating as two things what are actually one. "Irreducibly complex", as I understand it, IMPLIES that there are no such series of viable steps to arrive at the result. As I understand, that IS the definition itself.

If were to build a radio, there would be a long series of assemblages before the "payoff" of a working radio. Even if one could conceive of other uses for the parts. That's a hallmark of intelligent planning: many successive apparently-useless intervening forms before some complex result is achieved.

Look, Behe's classic example is the mousetrap. Certainly, cheese is useful in other contexts. Certainly, wire is useful in another context. Certainly, boards are useful in other contexts. Yet even if we put cheese, wire, and boards into a room, allowed secret "process X" to run for an indeterminate (possibly long) time, and found a mousetrap, we'd conclude the mousetrap were designed: there are too many non-viable steps between "board" and "board, bent-wire-with-spring just-so, attached here, loaded with cheese" to conclude otherwise.

Now, of course, we certainly can hypothesize some Lego-like system where larger and larger "useful" components get built up and swapped among systems. And of course, IC critics are welcomed to supply the details, if that's feasible. But in the absence of such, then we could say CURRENTLY, the best evidence seems to show such systems have the characteristics normally associated with designed entities.

As far as I can see, that's where we currently stand, no? IC critics say (as you seem to be saying above, with parts A-E) that perhaps such a scenario could occur. Right. Perhaps. But the proof's in the pudding, isn't it? Exploring that idea (see last link in previous post) can help flesh out how likely or unlikely such a scenario seems to be. And, at some point, we have to draw some (at least tentative) conclusion from evidence, not merely hopes. And the evidence (I'm submitting, just to try defending it again) seems to currently demonstrate IC, for this particular component.

(Again, if Dawkins and co could run around implying so-called "Junk DNA" seems to prove their view (though it didn't), even though we hadn't even begun to study the stuff — then why is it reprehensible to draw a similar conclusion from what is currently known about the flagellum? "Junk DNA" advocates certainly felt free to draw tentative conclusions based on current evidence. Why not also do so with flagellar complexity? Because one tentative conclusion was, for them, "right" and "agreeable" and the other would be "horrific to contemplate.")

If the purpose of arguing for irreducible complexity is only to argue that precursors of flagella might not have functioned as flagella...

I think I've addressed this in the previous section. Also see the aforementioned link.

The issue for Darwinian evolution, however, is not that a car with wires removed can't drive, but whether it can perform any function whatsoever. The body of the car might make a suitable home, for instance, with the engine functioning as some form of heater...

Did you read my "hillbilly salad bowl" argument? That's exactly my point. In the case of the flagellum it seems the assembly "rolled off" the larger, functioning unit and was repurposed. But that doesn't give us an evolutionary path back from hubcap to car (or from assembly to flagellum).

First, a salad is served in the hubcap. Fine. Then a tire is stuck over the "salad-containing" end of it. Okay, what's this good for? Then, an axle is attached to the tire. Okay what use has that... ?? Then... ??? Then...?????

The Discovery Institute, which you linked to, seems to flirt with this error ... "... most of the critical intermediate structures perform no function for selection to preserve."

I'm not seeing an error here. Is the statement, based on current evidence, true or false? If not clearly false, then what error?

So while the Discovery institute is arguing for Intelligent Design rather than God it seems to abuse IC in the common fashion, by assuming that all evolution is what Behe terms "direct evolution."

Huh? I've never heard any such thing from them. Most their proponents admit that micro-evolution works just fine, and I expect not a few agree there are transitional forms. Even Behe (as I understand him, not having read him directly) only purports to offer a few examples.

You seem to be switching roles here. It isn't, say, theistic IDers who have to prove EVERY example conforms to design. Indeed even if I wanted my theology preserved at all costs, I'd still be open to everything from Darwinsim to special creation, if requisite evidence could be produced. It is, to the contrary, Darwinian materialists who cannot allow even a single exception to the own rule. All Behe or some other IDer has to do is claim and produce one example (life itself, the Cambrian explosion, the flagellum, the universe) and the game's up.

Dembski does make the interesting argument that the TTSS may have evolved from the more complex flagelar apparatus...

My understanding is that the flagellum is known as far older than TTSS, which suggests to me that TTSS may have been produced by repurposing a broken part of TTSS code from an infected cell. Predators always arise after their prey.

... that the modern flagella contains a type of secretory system in it.

Again, Miller himself, bold added: "On the basis of these homologies, McNab (McNab 1999) has argued that the flagellum itself should be regarded as a type III secretory system." In other words, we should consider it one only because it LOOKS a bit like one, not because it functions like one. By the same token, I should argue that certain high-end hubcaps should be regarded as an outgrowth of the food preparation industry, because some clearly seem homologous to salad bowls. ;-)

And, again, look at end of my last comment to notice how little one actually even "looks like" the other. The TTSS seems to be a part of the flagellum with a lot of the information/functionality removed or crippled. A hubcap used for serving salad, if you will.

Posted by: Tim (Random Observations) on July 12, 2009 04:45 PM

Immunogenicity and protective efficacy of three Campylobacter jejuni flagellum-secreted proteins, FlaC, FspA1, and FspA2source

The TTSS seems to be a part of the flagellum with a lot of the information/functionality removed or crippled. A hubcap used for serving salad, if you will.

Ryan: The more general form of the argument, however, that the flagella could have been formed from some type of secretory system, seems quite reasonable considering that the modern flagella contains a type of secretory system in it.

At the very least, this should overturn the discovery institute's claims that the components of a flagella don't serve a useful function.

(I'll read the links that you gave later today or tomorrow. Thanks!)

Posted by: Ryan W. on July 13, 2009 12:02 PM

Posted by: Ryan W. on July 13, 2009 12:18 PM

Huh? Here's Dembski:

In place of [specific] proposals, Darwinists simply observe that because subsystems of irreducibly complex systems might be functional, any such functions could be selected by natural selection. Accordingly, selection can work on those parts and thereby form irreducibly complex systems.

Sounds like he understands your objections better than you understand his.

At the very least, this should overturn the discovery institute's claims that the components of a flagellum don't serve a useful function.

Once again, that's a straw-man representation of the IC argument. I just quoted Discovery admitting that components of a flagella could serve a useful function. I also just spent numerous paragraphs, in my first response above, explaining that Miller's use of the same argument is a false representation of the IC argument. I gave an example argument (hillbilly hubcap) which showed how one could be true without the other. I also gave you three links, each of which addressed the issue.

I have no idea about what else to do to communicate that idea.

The IDers would need to propose some other model which was more predictive than a materialist Darwinist one.

7. On one hand, in a rather general sense (perhaps more general than some would prefer), they have. They say we should explore and think about certain biological systems as though they were engineered, and software-based, rather than structures which arose by chance.

(You might say that's not specific, but I'd argue it's just as specific as a conviction all things have a natural cause. For example, as I mentioned recently, a number of Darwinists predicted "junk DNA" would have no useful function, based on their conviction that the "blind watchmaker" would necessarily leave a lot of detritus lying about. Conversely, it was ID proponents who predicted it would probably have a use. ID proponents won that particular bet.)

On the other hand, I'd argue they serve a useful function regardless. Normally, one DOES want some detailed model. But there are situations where the scientific community backs itself into a corner with a partial, wrong, or overapplied model, and, at that point, simply being critical of orthodox dogmas (that is, pointing out specific weaknesses) is the first necessary corrective step.

This may happen (and has) long before it's technologically possible to begin to explore or describe the alternative.

Consider quantum physics. The prevailing view (determinism) said particles behave in predicable manners. Quantum theory said that God rolled the dice out of sight, that there were NO ways of predicting specific events. So a detailed theory which promised specific predictions was replaced with a giant question mark. And even now, we have no clue as to how the vast majority of physics works. And, unlike most biologists, physicists seem comfortable with the situation, and are just fine admitting: "We don't really know the answers."

Finally, if certain events WERE "miraculously" improbable, then there IS no testable alternative theory. You're asking for an impossibility. I mean, seriously, replace "flagellum" with an "alien artifact":

X: This design came about by chance.... the movement of the water and wind formed it.

T: I don't think you could explain a kind of erosion which produced THAT shape. If you think I'm wrong, demonstrate specifically how wind and water could have formed that.

X: Well, what's your alternative theory?

T: I don't know. Perhaps an alien produced it. Or a previous human visitor, long ago. Or a deity.

X: You're not giving a specific theory!

T: True! My theory IS even vaguer, in a sense, than yours. And so? I'm proposing that if we can't find a natural way of explaining something, or even can prove it improbable beyond a certain degree, (or other criteria X, Y, Z) we should consider it a sign of intelligence. (Produces more arguments, and perhaps some equations showing improbability.)

And even if I'm wrong, it still doesn't negate your need to back up your own argument with specifics. The default position could be "we don't know" rather than all this asserting of our fond hopes as fact.

Last, if it was created by an intelligence, we wouldn't necessarily know how, specifically. For example, if I found PI written out to 100 digits in binary, I wouldn't know whether it was done on a computer or with a manual process, measured directly, done by aliens, by a human (of what race or nationality), by God, or what. I also might not know what was used to carve the markings. We don't have to know specific details about the source to identify products of intelligence.

8. I should probably also explicitly address the Musgrave article you posted earlier. I would yet again beg you to read the third link (Pitman) posted in my first response, which answers many of the conjectures raised by Musgrave. For example, Musgrave:

The protoFLiG was originally a support system for the transport machinary. Adding the MotAB system to the protoflagellar complex adds protons to drive the transported substrates faster up the hollow rotor. Then a mutation alters protoFliG so that proton acceptance by FliG causes one of the arms of the Y to rotate (as seen in other molecules), then this would rotate the rotor, and hence the filament, and motion commences. As I said this is speculative, and a more detailed analysis of FliG and the FliG homologs, plus other components of the system, is needed to get a clearer picture.

In contrast, Pitman describes FliG in detail (noting, contrary to the above, there are no FliG homologs), and concludes:

.... This means that Metzke's assertion that FliG, as part of the proto-secretion complex, is "retained only in order to stabilize/support the coadapted secretion complex and the FliF ring, and [is] otherwise vestigial" is complete nonsense. FliG is vital to secretion and has nothing to do with FliF stabilization (FliF has been shown to be quite independently stable). It is just that FliF without FliG cannot form an adequate flagellum.

The devil, as they say, is in the details.

Posted by: Tim (Random Observations) on July 16, 2009 02:27 AM

How is this mindless non-directed creation accomplished? Through the creative powers of random mutation and natural selection. ( Back to Top ) detecting design

As a sidenote, mutations prior to selection don't seem to be equii-probable throughout certain genomes. I'm familiar with this in viruses, where the viral coat mutates rapidly while other areas are conserved, prior to selection. Because of this I'd argue that while variation has a random component, it is not entirely random ( like replacing drill bits on a drill, but keeping the base static. ) Also, expression of certain genetic mutations seems to be inducible by stress as some sort of last-ditch effort on the part of the organism. The process is fairly recently discovered and doesn't seem to be well understood, but interesting all the same.

Most of an enzyme's bulk seems to be structural. A small portion, the active site, could be modified rapidly to get new catalytic activity. Any probability analysis of the liklihood of a certain mutation would need to consider whether an enzyme might have been formed in this fashion. The only thing needed to develop such a functioning enzyme in a remarkably short time would be some kind of feedback mechanism that recognizes when a molecule has been bound and/or catalyzed. The vertebret adaptive immune system seems to work on a similar principle, and has been employed to create catalysts. source for the existence of this process on page 125-6 of linked book. I haven't read the whole thing
(IIRC from college, antibody catalysis required knowing the transition state of the desired reaction beforehand, which would take more intelligence than seems reasonable for a genetic mechanism. A non-teleological mechanism may take many times longer, but might still be tremendously faster than truly random mutation.)

...Alternatively, the ion pumps became linked to the proto-flagella to provide extra "power" to pump proteins out of the complex ... Eubacteria (and most cells) express a number of ion pumps to help keep ionic balance in the cells, these can become loosly associated with other protein complexs to provde electromotive force to the other proteins. Association of the proto Mot ion chanels with the protoflagella is not a difficult or unlikley step.muscgrave paper

It's not conclusive that this did happen, but certainly probable that a powered secretion system (a motorized pump) of some type pre-existed the model flagellum in question. From the standpoint of 'IC' this is certainly a possible route.

From your "detecting design" link; This sequence has to be just right to work for many types of high-level functions.

Very few sequences have to be 'just right.' Most can have thousands of variations and still function.

Re: the definition of IC

Three definitions are summarized by the International Society for Complexity, Information, and Design:
1. Michael Behe's Original Definition — [an irreducibly complex system is] "a single system composed of several well-matched, interacting parts that contribute to the basic function of the system, wherein the removal of any one of the parts causes the system to effectively cease functioning." (Darwin's Black Box, page 39)
2. William Dembski's Enhanced Definition — "A system performing a given basic function is irreducibly complex if it includes a set of well-matched, mutually interacting, nonarbitrarily individuated parts such that each part in the set is indispensable to maintaining the system's basic, and therefore original, function. The set of these indispensable parts is known as the irreducible core of the system." (No Free Lunch, page 285)
3. Michael Behe's "Evolutionary" Definition — "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."

source

Note that Behe's original definition of IC is function dependant, which precludes a change in function of the system during the course of development. I feel I've documented this pretty well.

Are we in agreement that by the definition of IC a system could be IC and still evolve via a coopted route by Behe's definition? My concern here is that the vauge definition of IC allows for statements by prominent IDers to sound stronger than they are. Behe makes one statement about a system being IC and followers parade that as evidence he's making a statement disproving Darwinian evolution. Which he's not.

“Even if a system is irreducibly complex (and thus cannot have been produced directly), however, one can not definitively rule out the possibility of an indirect, circuitous route. As the complexity of an interacting system increases, though, the likelihood of such an indirect route drops precipitously. (Michael Behe, Darwin’s Black Box, pg. 40)

These are Behe's own words, no?

You quoted

one could find a sub-part that could be useful outside of the final system, and yet the total system would still face many points along an "evolutionary pathway" where it could not remain functional along "numerous, successive, slight modifications" that would be necessary for its gradual evolution.

So yes, Behe does give a head nod to co-option in DBB. And Dembski notes that showing that screws can evolve independant of a machine is not a refutation of IC of the machine. Granted, and some of his critics probably actually made that argument, so his clarification is necessecary. He addresses cooption in this very narrow sense. But I've yet to see the issue of co-option of a complex system suitably engaged and refuted, which is odd given that they seem to dismiss the possibility so strongly. Perhaps one of these fellows has written something that I just haven't seen. If you find such an article, please post.

It's also addressed in a number of other points in the accompanying link. The second link, as well, also has a discussion (by Dembski, another member of Discovery) of the co-option argument. And the third link (did you look at it yet?) deals also with the issue extensively.

I've read through the detecting design article. It was probably one of the best, most rational articles that I've seen so far. But it does still seem weak on the topic of co-option. We have pages of in depth analysis followed by the assumption that centripital force is the only force capable of moving a protein through a hollow tube. As if the author never used a straw? Maybe I'm missing something horrificly obvious here about the force required.

If any of one of these parts went missing or became altered beyond a certain fairly constrained degree, the overall function of the system (motility in this case) will not work at all - not even a tiny little bit. detecting design article

A pump off the back of a boat can provide motility by itself.

R: Also, for IC to be falsifiable there needs to be a positive statement about what the core system consists of.

T:4. Not at all. If you can show a path of slight modifications leading from far more common and less complex parts to the flagellum (yes, including co-options) then, at least as far as I'm concerned (and probably most observers), the IC of the flagellum would stand falsified.

Okay, granted I should have said that much, much differently. But if it isn't possible to clearly state which portions of an organism are IC doesn't that, in itself, say something about our ability to 'recognize design?'

Huh? Here's Dembski: In place of [specific] proposals

Your link goes back to your site. And I'd note that the passage you cited doesn't do anything to refute cooption as a possibility.

Once again, that's a straw-man representation of the IC argument. I just quoted Discovery admitting that components of a flagella could serve a useful function.

I also just spent numerous paragraphs, in my first response above, explaining that Miller's use of the same argument is a false representation of the IC argument.

I have no idea why. I've already noted several times that Miller's didn't seem like the best argument out there.

I just quoted Discovery admitting that components of a flagella could serve a useful function.

There are several statements made by IDers in regards to cooption;

First, saying "an IC machine can have screws in it, and those screws might evolve separately, but do not prevent the machine from being IC," which the discovery institute has said and which is true, almost by definition.

Second, saying "An IC machine could, with reasonable probability, be evolved from an extant, complex coopted system of a different function" which I would agree with, but tends to make an absolute hash of those strong claims IDers have made of IC as a Darwin killer.

Third, saying that cooption is improbable. I've seen this assertion made, but consider the support for it to be grossly inadequate, especially given the relative rigor of surrounding detail some of the articles seem to have.

7. On one hand, in a rather general sense (perhaps more general than some would prefer), they have. They say we should explore and think about certain biological systems as though they were engineered, and software-based, rather than structures which arose by chance.

I'm open to that, provided that 'engineered' is not the same thing as 'teleological.' The question here, for me, is the degree to which the genetic code is seen to be capable of 'planning' things as opposed to using blind tricks like altering the active site of an enzyme (possibly with feedback) rather than the whole genetic code for it. If they're merely arguing against 'purely random genetic variation' then I agree completely as noted in this current posting and think the evidence is on their side.

In other words, I see a difference between 'intelligent trial and error' and 'design.'

T: True! My theory IS even vaguer, in a sense, than yours. And so? I'm proposing that if we can't find a natural way of explaining something, or even can prove it improbable beyond a certain degree, (or other criteria X, Y, Z) we should consider it a sign of intelligence. (Produces more arguments, and perhaps some equations showing improbability.)

As a hypothesis, it may be interesting. But until this theory can be shown to be predicitive in some way, I'm not sure what value it has.

I've read the Pitman article, but may have to go over it again at some point in comparison with Musgrave.

The paper discussed here, by Matzke, is no exception. Matzke makes no attempt to calculate the odds of evolution crossing any of his proposed steps in the flagellar evolution pathway.detecting design

One problem with 'calculating the odds' seems to be, in part, that it assumes a teleological method; that evolution was 'trying' to design something specific. What if the possible number of targets are not known? Such a method will be consistently biased towards improbability.

Posted by: Ryan W. on July 21, 2009 02:39 PM

Posted by: Ryan W. on July 22, 2009 09:37 AM

In vitro, flagellar filaments assemble spontaneously in a solution containing purified flagellin as the sole protein. [link]

And how, precisely, did that situation arise? Etc...

I'm a complete layman, but I've seen various kinds of presentations on a number of systems, and the subjective impression I get is that they do boggle the mind quite a bit. Even a simple eyespot goes through quite a number of complex transformations to react to light, for example.

Why wouldn't a powered pump be able to create enough flow to move folded proteins down the tube?

I assume it's true, because nobody's saying otherwise, but just a wild guess, for fun: look at the shape of the protein in question: They don't look "pushable" -- they're bent and curvy, and would seem likely to snag or snarl if pushed from behind (I think I recall reading something to that effect), rather than "pulled" by their own mass.

I'm not familiar with the details of how substances behave at that level...

Frankly, me neither, but it doesn't seem to be a hotly-contested point, as best I can see.

mutations prior to selection don't seem to be equii-probable throughout certain genomes...

I'm not sure what you mean by emphasizing "prior to selection", but I'm aware some sites mutate far more easily than others. I agree entirely. I also agree (as you ought to well know) about environmental influences triggering or altering expression (or affecting some non-genetic yet inherited factor which alters expression). (See the earlier post on Podarcis sicula, in which lizards seemed to produce an entirely new species with (allegedly) no mutations.)

There's much more in this section I'll have to digest later for an intelligent response.

Very few sequences have to be 'just right.' Most can have thousands of variations and still function.

In many cases, I don't doubt that.

But the author gives specific examples which correspond to the analogy in that section. For example:

Of course, the FliG protein (with no significant homologous counterparts by the way) is also the subpart responsible for converting the proton-motive force into torque forces for the rotating motion of the flagellum. The ~100 C-terminal residues seem to be required for this function to be realized. In addition, specific mutations to segments 10, 18, 19, 24, 25, 28, 29 and 31 formed flagella, but were paralyzed.

The degree of "just rightness" is essentially the number of "useful" permutations out of the total space, weighted by the probability of reaching each. I'm not sure all (or any?) such numbers are currently knowable, but he's providing a reasonable-sounding case, for many examples he gives, that there isn't a lot of fault-tolerance allowed.

Of course, one might speculate there are other "ghost" assemblies which perform essentially the same function, which should be included in the probability space. Perhaps they're even more efficient and simple and appropriate for the attached organism. Perhaps. Or maybe not. But it seems to me we have to draw actual (if even tentative) conclusions based on what we know, not just hopes.

Note that Behe's original definition of IC is function dependant... I feel I've documented this pretty well.

I see that now, and readily concede the point. Great historical-info link, by the way.

Side note: I agree that Behe's original definition was pretty weak (the link shows how using similar example to my admission above). In my first comment, I almost explained I wouldn't be defending Behe, but more IC as I understood it.

Another side note: I find it interesting the same people who slam Behe for an "evolving" argument for IC readily accept the exact same process in other areas. Darwin isn't laughed at because of neo-Darwinism has revised and fixed many weak arguments, for example.

But I've yet to see the issue of co-option of a complex system suitably engaged and refuted...

I feel like we're talking past each other here. ID critics (and you, now) keep saying: "You haven't refuted this." Yet (a) where specifics HAVE been proposed, ID proponents seem to do a good job of addressing and (apparently) refuting them (e.g. Matzke/Pitman, Miller), (b) where specifics haven't been proposed, I don't see that any more burden of proof falls on ID proponents than their critics. To the contrary, given that most the systems they cite SEEM, subjectively, incredibly improbable, it would seem their opponents have more a burden (an unsatisfied one at that) than they do.

To me, the conversation looks like this:

IDist: Look, this seems impossible!
Darwinist: Oh, no, perhaps co-option produces it! (Suggests vague scenario A)
IDist: Look, there are serious holes at the specific points suggested (xxx), and still gaps between them.
Darwinist: You still haven't utterly eliminated co-option (etc)!

The Darwinist thinks his case should be accepted as almost certainly true (i.e. "true") until all all unspecified scenarios are eliminated and disproven. Meanwhile, the ID case can't be evaluated even on the basis of existing data. It's not even allowed, apparently, to just agree to differ. No, the one offering imaginary scenarios must win absolutely, and those pointing to actual examples must lose. Academically, co-existence is not an option.

Doesn't that strike you as more than a tad odd?

But it does still seem weak on the topic of co-option.... [later:] the passage you cited doesn't do anything to refute cooption as a possibility.

This illustrates my point exactly. It's not Pitman's job (nor mine) to imagine his own co-option scenarios, and then refute them. His piece exists to refute Matzke's specific proposals. It is the responsibility of those who argue "co-option did it" to produce evidence to that effect. It is not the job of their opponents to first do their work for them.

I mean, seriously, Ryan, does such pass as reasonable form of argument in any other area? The theist is right until the atheist imagines all the ways the atheist himself might be wrong and utterly excludes them?

Tim: I also just spent numerous paragraphs, in my first response above, explaining that Miller's use of the same argument is a false representation of the IC argument.

Ryan: I have no idea why. I've already noted several times that Miller's didn't seem like the best argument out there.

The italics above that indicate I was responding to your (incorrect, it seems to me) claim that "discovery institute[] claims that the components of a flagellum don't serve a useful function." That's the same straw man Miller employed. How can you say "Miller made a weak argument" and then repeat it, apparently seriously, as your own?

A pump off the back of a boat can provide motility by itself.

Only in a rhetorical sense. If the boat must cover enough territory (or haul enough weight) to collect enough fish for its passengers to survive or thrive (or merely justify the expense of the craft), not. Likewise, I'm sure a hole in the bacterial membrane would propel it in a certain direction — while its contents leaked out, and, ignoring that, probably not at a rate which would allow it to perform functions necessary for survival.

Second, saying "An IC machine could, with reasonable probability, be evolved from an extant, complex coopted system of a different function" which I would agree with, but tends to make an absolute hash of those strong claims IDers have made of IC as a Darwin killer.

Citation? What ID proponent is saying that the bacterial flagellum could have evolved, "with reasonable probability", via co-option?

Third, saying that cooption is improbable. I've seen this assertion made, but consider the support for it to be grossly inadequate...

Again, citation? Which ID proponent is saying that co-option is improbable? I'm not seeing anything of the sort.

Perhaps you mean to say that they feel it is improbable that the flagellum could occur by chance, even considering co-option? See arguments above, if so.

I'm open to that, provided that 'engineered' is not the same thing as 'teleological.'

Since, last I checked, "teleological" is simply a synonym for "designed", I don't even understand this introduction...

The question here, for me, is the degree to which the genetic code is seen to be capable of 'planning' things...

I assuming you're just changing the topic, here, no? Neither IDers nor their opponents believe DNA "plans" even small aspects of its future. If so, I should have taken this on when you first mentioned it, as now it will be buried in a much longer (perhaps too much longer) response:

I don't think there's anything "parsimonious" at all about the idea that there's a non-trivial kind of "intelligence" which operates at the genetic level. One complexity simply begs the next: if DNA was "smart" enough to somehow build the flagellum, then that 'software' is at least as complex (and thus improbable) as the flagellum itself. (Probably moreso, as it contains the potential for many such flagellum-like structures in itself, and the means of building it.)

In other words, I see a difference between 'intelligent trial and error' and 'design.'

I realize you probably think you just explained it, but I'm not seeing it. I work as a software developer. I do "intelligent trial and error" all day long. It is the "intelligent" aspect of that which makes it also "design". Perhaps you could explain something which was created by an intelligence, but not designed.

I'm trying: let's say I punched a hole in wall by accident. Certainly, I'm intelligent (some days, anyway), but I didn't intend to make the hole, so it wasn't designed. But how is that any different that if a small asteroid hit the wall at the same place? I'm just not following here.

... until this theory can be shown to be predicitive in some way, I'm not sure what value it has.

I dunno: is it important at all to know if anything in the universe, or the universe itself, was designed or by accident? I expect the results of such would indeed be important.

But you're acting as though I just admitted "design" isn't predictive at all. No: I was doing my usual layering thing of making point A, then assuming we didn't have point A, but showing that still led to point B, then assuming, charitably, those weren't true either, to still make point C...

But I had just mentioned examples where assuming design yields results: junk DNA and cellular informatics. There are countless others: people who believed in "design" thought the universe would have had a start. Right again. The complexity of life. The scarcity and improbability of life. The fine tuning argument. These are all things that materialistic scientists were betting against, based on their assumption of unguided materialism, early in the 20th century.

In fact, I'd argue (as you're surely familiar) that science as a whole owes its existence to the assumption of design. Only in the West, where scientists believed unknown physical "laws", analogous to God's moral laws, must govern the behavior of things, did science arise, as a direct result of a pervasive assumption of design.

More specific? Francis Collins, in The Language of God, takes ID to task for not allegedly producing testable predictions. Then, the spends time attempting to show that the blood clotting mechanism isn't IC. Well, which is it? If you feel you can show it's wrong, then it certainly is a testable prediction. (BTW, I'm not conceding I agree with Collins' argument regarding blood clotting.) Similarly, I suspect quite a bit of research on the flagellum has been spurred mostly or even solely out of a desire to finally prove Behe wrong. Again, that's certainly valuable no? (You seemed to agree when you said prizes or bets can spur research, and seemed to agree IC could be treated as such. Now you seem to be backtracking.)

When Fred Hoyle was trying to figure out how carbon was created, he realized he had to approach it as a engineering problem; he figured out how he would have done it, and thus deduced (fairly accurately, it turned out), there had to be an undiscovered (and surprising) resonance level for Carbon 12. I believe this is the incident which led to him famously complaining the universe seemed to be a "put up job." Hoyle, later:

A common-sense interpretation of the facts suggests that a superintellect has monkeyed with physics, as well as with chemistry and biology, and that there are no blind forces worth speaking about in nature. The numbers one calculates from the facts seem to me so overwhelming as to put this conclusion almost beyond question.

(More details here, with apologies for the over-exclamatory capitalization of that page.) (Subjectively, and only half in jest, I think an assumption of design might also have predicted this particular irony was to be inflicted on Hoyle, an atheist who had done probably more than any other to stave off the horrifying "Big Bang", as he derisively named it.)

One problem with 'calculating the odds' seems to be, in part, that it assumes a teleological method; that evolution was 'trying' to design something specific.

First, you're misplacing the modifier. "Evolution" wouldn't necessarily be the designer "trying" to achieve some result. (I don't see how "evolution", which is an abstract explanation, could have a brain, intent, etc. Where would it's sense of sight be, for example?) The one "trying" to produce the outcome would be some sort of deity, or aliens, or perhaps something else we hadn't thought of.

And if you disregard signals from (im)probability here, using such a feint, then how can we retain them elsewhere? We normally use measures of statistical confidence to distinguish all sorts of meaningful events from noise. When a statistician "calculates the odds" of getting a straight flush, he isn't assuming the cards are "trying" to achieve some hand. Yet if a dealer dealt straight flush after straight flush from the top of each seemingly freshly-shuffled deck, we'd quite reasonably conclude something more than "random chance" was likely afoot, no?

So why does that allegedly turn into a fallacious scenario if we substitute "DNA" for "cards" and "history" for "dealer"? One tip I use for spotting twisted thinking is to try substituting simpler, less-loaded nouns. Does the form of argument still make sense? If you can show a meaningful distinction lost or gained the switch, great. If not, then one's thinking may be suspect.

What if the possible number of targets are not known? Such a method will be consistently biased towards improbability.

So if we don't know all the possible targets, we should then assume in favor of the one positing them? Such a method IS consistently biased towards those positing them. And IS accepted today, apparently. (You seem to be accepting it, for example.) That is at least as fallacious, and, I'd argue, more so.

As I said above, in most cases, it's impossible to exclude the possibility of unknowns. Perhaps there are unicorns on earth, right? Perhaps there are huge hidden reserves of oil every single place we haven't drilled yet. This doesn't stop people from drawing reasonable inferences.

Except in biology.

Where such mundane logic must be reversed.

Because something big is at stake.

Materialism.

What if "peak oil" were a biological argument? It would sound like this:

Some fools say we'll someday run out of oil, because they calculate the amount from known reserves. But, after all, we don't know how many total, possible, undiscovered sources of oil there may be. Such a method will always be biased towards scarcity! Why, perhaps there are vast reserves of oil in every single place we've never drilled! Or perhaps it will fall from the sky tomorrow and every day afterwards! Peak oil enthusiasts will have to engage my arguments, figure out how they might be true (not my job!), and then roundly disprove each and every one of them! Otherwise, I must be right!

Now, I actually argue against Peak Oil. But I'd never do so using the form above, which is an argument from non-evidence. Instead, I point to real historical trends: Oil reservoirs have refilled, meaning there's more oil than we estimate. Estimates of reserves have continually increased, rather than decreased. And technology has delivered new types of energy, and more efficient uses for it. *I* supply this evidence, as is my burden: I don't demand my opponents think it up for me.

Historically, it seems to me, the historical trend goes the wrong way in biology: Life keeps ending up being more complex and improbable than everyone first assumed. Existing puzzles and problems have been replaced with ever weirder sub-problems. Once, as I say, cells were bags of liquid. Now they're tiny cities whose software is written in a "langauge" or "code" -- terms, in our experience, always associated with intelligence and engineering.

One can reject rationality -- that is, one can reject all signals from probability, and refuse to draw any conclusions from tentative evidence. (And evidence is always tentative, isn't it? How does a court know if it's seen all possible evidence? They don't, of course.) One can offer completely contradictory standards of proof, depending on the desired outcome.

Or one can be intellectually consistent with the way we live the rest of our lives, drawing tentative conclusions based on available evidence, but keeping an open mind.

Except when materialism is at stake! :

"Junk DNA" should be presumed to have no functions immediately, before we've even begun to explore it. By materialists. Who then beg and plead please not to exclude (indeed, quite the opposite!) undiscovered roles co-option may yet, hopefully play in forming the bacterial flagellum. Because in one case, if something is unknown, it's certainly not there, in the other case, if it's unknown, it's practically a proven fact until someone shows otherwise.

Again, doesn't this all seem just a tad absurd?

Posted by: Tim (Random Observations) on July 26, 2009 05:49 AM

Posted by: Tim (Random Observations) on July 26, 2009 02:42 PM

I'm going to reference propulsion in gliding bacteria which are not strictly related to the topic. But while little seems to be known about the mechanism of propulsion in gliding bacteria (and it may be more complex than evidenced here) it seems that they move forward via extrusion of slime, which would at least indicate the possibility of a secretory system providing functional propulsion, especially if the purpose of propulsion is population dispersal. http://content.karger.com/ProdukteDB/produkte.asp?Aktion=ShowFulltext&ProduktNr=228391&Ausgabe=230059&ArtikelNr=77871">source

If you agree that creatures can evolve quickly and with few apparent mutaitons (vis a vis the lizards on the island that you've mentioned) then why couldn't this suggest a genetic intelligence? There do seem to be genetic feedback mechansisms, such as heat shock protiens, which indicate that a system is stressed. If we're to anthropomorphize such a mechanism to be able to discuss it more readily, I don't think the genetic "senses" would be things like sight, hearing, etc. but things more related to the state of the organism internally like "hunger, stress, toxicity" etc. And possibly even mental stimulation

And if you disregard signals from (im)probability here, using such a feint, then how can we retain them elsewhere? ...When a statistician "calculates the odds" of getting a straight flush, he isn't assuming the cards are "trying" to achieve some hand.

First, a statistician can only calculate odds when certain things are known such as the number and type of cards in the deck and the number of cards in a hand. To calculate the odds of winning, the value of all (or at least most) possible hands must also be known ( calculating odds of winning are much less reliable if someone could beat a straight flush with a surprise two, a four and an ace, say, and if such upsets were reasonably common. They are also less reliable if we've only seen one game (universe) ) To see signals from improbability elsewhere, I'd think similar conditions would have to be met, or be close enough to being met that there isn't enough uncertainty left in the system to overwhelm our predictions.

But I've already agreed with the assertion that changes to genetic code are likely not 100% random chance based on viral mutation rates and locations (which are simple enough that I think we could make some plausible assertions using the above critiera.) The question, then, is what the non-random pattern looks like and what its source(s) and mechanisms are. When ID can propose some mechanism, (which I think someone, ID or not, will do this eventually), it will deserve a lot more credibility as a theory as opposed to a 'bet.'

So if we don't know all the possible targets, we should then assume in favor of the one positing them? Such a method IS consistently biased towards those positing them. And IS accepted today, apparently. (You seem to be accepting it, for example.) That is at least as fallacious, and, I'd argue, more so.

"Random chance" is usually a null hypothesis to be disproved. If Behe wants to assert that something is non-random then yes, the burden of proof is upon him. If we don't know how many targets exist in a field, it's impossible to tell via probability if an archer aimed his arrow or hit one randomly.

Tim: Perhaps there are unicorns on earth, right?

Ryan: Right!

Perhaps there are huge hidden reserves of oil every single place we haven't drilled yet.

In this case, we at least know our target, oil. But what if we said "Perhaps there's substance of value everywhere we drill. What's the probability of that? It's a much more nebulous question to answer using probability, because it's harder to know all possible substances of possible value.

( What I'd really like to see is a demonstration of some kind of observable, repeatable mecahnism, material or otherwise, in regard to this topic. )

Parody argument Tim: Some fools say we'll someday run out of oil, because they calculate the amount from known reserves. But, after all, we don't know how many total, possible, undiscovered sources of oil there may be. Such a method will always be biased towards scarcity! Why, perhaps there are vast reserves of oil in every single place we've never drilled! Or perhaps it will fall from the sky tomorrow and every day afterwards! Peak oil enthusiasts will have to engage my arguments, figure out how they might be true (not my job!), and then roundly disprove each and every one of them! Otherwise, I must be right!

If you repleace the word "oil" here with "energy" I'd agree with the argument for the most part. Are we at peak energy? Noone knows and noone can know. It is a very tenuous thing to assert. I'd suspect we're not. I see the IC argument regarding the flagella as more analogous to 'peak energy' than 'peak oil.'

Once, as I say, cells were bags of liquid. Now they're tiny cities whose software is written in a "langauge" or "code" -- terms, in our experience, always associated with intelligence and engineering.

Some form of genetic code was assumed long before it was discovered, incidentally. That the code is common to almost all creatures (and RNA is similar enough) was something of a victory for evolutionists. Origianlly, people were looking at protein as the possible coding substrate since it seemed more complex. DNA was actually a much simpler molecule. (Though there's an insane amount of the stuff even in a small cell.)

further supported their conclusions by showing that this ‘transforming’ activity could be destroyed by the DNA-digesting enzyme DNAase2,3. This work first linked genetic information with DNA and provided the historical platform of modern genetics. Their discovery was greeted initially with scepticism, however, in part because many scientists believed that DNA was too simple a molecule to be the genetic material. source cited only to document the assertion. I haven't read the rest of the article

1. Only a rotating flagellum is known to provide effective means of mobilizing unicellular animals of that size, given their niches.

Size and niche can change over time.

2. The mechanical efficiency required for survival would have to be similarly high as existing flagellar systems.

Why? That's not even true for all modern organisms.

But when you inspect them closely, it turns out that nothing could fulfill that role which isn't also similarly complex.

So life must be teleologically designed because a teleologically designed system is the model?

One might say: "Well, the problem doesn't HAVE to be solved. There was no intent there." On the former: Doesn't it? Life exists, after all. One can resort, again, to ir- or a-rationality: "Well, everything 'just happened' with no cause, and evidence means nothing." Fine. Have a nice day. I respect you, but have nothing to talk about, any more than with a solipsist. Like Marxists, such individuals operate in spaces which are unreachable by evidence.

As I mentioned earlier, I'd like to see IC demonstrate some kind of observable mechanism before it is considered scientific. If we believe that the universe works based on certain laws, it seems at least fair to ask what those laws might be. After all, when improbable things happen do courts typically ascribe divine intervention? Whether such things happen, legal standards which looked to such intervention seem terribly unjust. Trial by fire, water, combat, etc. To the extent that IC advocates propose a non-regular universe (if they do) I think that there's a large burdern of proof resting on their shoulders.

Posted by: Ryan W. on July 28, 2009 05:55 PM

Posted by: Ryan W. on July 30, 2009 01:04 AM

Fair point! Forrest Mims (the genius who designed the toy which taught me to love electronics, and who was banned from Scientific American, in a rather shameful incident, because of unrelated religious views) seems to have predicted it back in 1994.

Dembski is also cited there as disagreeing (citing a maverick) back in 1998 — the same year that Dawkins was saying "creationists might spend some earnest time speculating on why the Creator should bother to litter genomes with untranslated pseudogenes and junk tandem repeat DNA" in his piece "The Information Challenge". (Hilariously, search engines are showing that 'sceptic' groups who once hosted this article have now pulled it from the 'net. :-) I wonder if they take their own 'challenge' as seriously as they were demanding of others. >;-))

But even if they hadn't, it would still seem to me it's actually enough for them to have stood by silently and wondered how it would turn out. "I don't know, let's look into more" is a right answer. "It has no purpose" is not.

Result above notwithstanding, this particular request, I think, implies a false dichotomy: Recall, ID proponents don't even say every single entity is useful. A space station may be littered with useless and damaged junk, but it doesn't imply it wasn't originally designed. So it's not the case that there are ID proponents running around saying: "Everything serves a purpose! And further, we'll discover every purpose!" Only the more vocal Darwinists in this particular story seemed to possess that level of surety. It was they who decided to stake out this particular ground.

If question Q resolves to in result R, a model which yields "Not R" is surely inferior to one which results in "Gee, I'd guess R, but I wouldn't stake my life on that."

(For another example, I'd again point to the TTSS/BF debate as another such example, where the evidence seems to be increasingly showing TTSS was derived from BF (or something similarly complex) not vise-versa.

Personally, I'd made the argument to my MicroBio professor back in college that the red dye of Serratia marcescens must have had some kind of utility or it would not be produced by a multi-part mechanism and be so widespread in the population. He disagreed and said it was useless. It turns out to have an antibiotic function. I did this at a time when my knowledge of evolution was pretty much 100% Darwinian...

Again, subtle false dichotomy: there are a spectrum of positions here. On one side, we have the IDers, convinced of ID, in the middle, we have people with various degrees of conviction on the matter (or perhaps mere scepticism towards the applicability of natural selection to all problems), and on the far end of the other side, we have the people some IDers call "Darwinbots", those for whom Darwinism isn't merely a mechanism, but a worldview.

You may have believed in the mechanism of Darwinian evolution (indeed, IDers don't even exclude it) but you hadn't absorbed some of the religious dogmas which (I would guess) informed your professor's (ahem) dogmatic insistence to the contrary.

I would guess your position was the same as my questions about Accutane. I wasn't being a "creationist" by asking such a question, but I was inadvertently touching on what was, for my doctor, a religious question.

There's more to address, but I'll have to come back to it later. Apologies, and best to you!

Posted by: Tim (Random Observations) on August 4, 2009 11:31 AM

Ah, yes. That was the broken link. Still broken, btw. I googled the passage and got
this exerpt from Dembski's book "The Design of life."

It complains that Darwinian explanations are abstractions bereft of details, and that function is required for a Darwinian mechanism to work.
Do IC arguments provide more details? Well, I've demonstrated that an unadorned secretory system can and does, in fact, provide the "function" of motility prior to being co-opted. Dembski does not seem to address that in the section cited, but only that a subsystem of an already IC system might be functional outside of the system. That's a crucial difference.

Here's Behe; So, only two possibilities are left: either sudden appearance of the complete machine (practically impossible for statistical considerations), or step by step selection for different functions, and with the target function COMPLETELY INACTIVE for natural selection. This is a point that Darwinists tend to bypass. Darwinists may believe in indirect Darwinian pathways, because it’s the only possible belief which is left for them, but it’s easy to see that it really means believing in impossibilities.

The third possibility is that a developed system also has a secondary function which can then be further developed at the time it was coopted. Behe seems to be ignoring that a developed system can have multiple functions, and that one which is poorly developed can be coopted for further development along a different route.
This seems to be the same as or similar to Dembski's stance. Instead, Behe seems to assume that a system developed for one purpose can have only one purpose and that other purposes must be developed later.

Yes, the components of a flagellum can have useful functions. That's agreed. And they could have had those useful functions to some extent when they were coopted, to some extent. That seems to be the point of contention, as far as I can tell.

As indicated previously, the portion of Miller's argument that I'm not bound to supporting is the modern TTSS - flagellar TTSS connection.

But what we have here, in the relevant fragment TTSS, is basically a hole with a rim around it.
well, you also have a system for producing and expelling materials and the related aparatus. A hole and a rim and a factory and a pump, if you will. But yes, it's basic. The starting point has to be basic.

There are steps missing, I agree. But IC is about preservation of function so I'm showing that a system could have a particular function when it was coopted, which Dembski seems to dispute in the article you cited where he
agrees that a subsystem of an IC system could have function outside the system. "A large difference in complexity" is not the same
as IC. IC is about function.

I understand you're referring to the immune system in vertebra. But I don't understand the connection to the topic at hand.

I'm trying to set up an analogy between the immune system, which is used to create catalysts in the lab (that's the connection to the topic at hand)
via rapid alteration of an antigen's active site and an enzyme with a hypervariable active site which could actually create catalysts in a unicellular population faster than
alteration of the whole gene for the catalyst would predict. This is why I hesitate when people discuss the probability of various things evolving. I'm concerned (without doing the math) that their assumptions could be wrong.

Tim: (a) The mechanism in question sounds a bit like a locksmith's saw, which produces a key to match a certain pattern. That doesn't mean the system which produces it can also churn out cars, transistor radios, and bilge pumps, or solve other generalized problems.

Granted, I'm not claiming it's the only mechanism at work here. And it's a hypothesis rather than a theory. But enzymes do serve a very wide variety of purposes within an organism. A system that could make a wide variety of enzymes (many possibly non-functional) would truly be a system capable of addressing a wide variety of problems, structural and chemical, or aiding with such.
Enzymes produce proteins and catalyze reactions for instance.

I've tried to describe how such a thing could be created relatively simply. Such a system, particularly if it could be coupled with some kind of basic feedback (and granted, that may be too complex to consider at first) would be capable of helping create a wide variety of adaptations in unicellular life.

why couldn't the Greeks give their kids simple names like "Bill" or "Steve"?

Dunno. Maybe last names hadn't been invented yet. You wind up with a classroom of 20 kids named "Steve of Miletus."

Re: info generation
If you think otherwise, and have evidence for such, I'd love to hear it.

What counts as evidence?

Re: Forrest Mims

Interesting. 1994-96 seems to be the start of the turning of the tide regarding views of 'junk DNA.'
There seem to be a fair number of publications addressing the topic 94-96. '96 particularly.
Mims picked up on it fairly early.
(Dawkins is conspicuosly late to the party. I think he made similar 'junk DNA' statements in '99 as well.)

"I don't believe in junk DNA," said Dr. Walter Gilbert of Harvard University, a pre-eminent theoretician of the human genome. "I've long believed that the attitude that all information is contained in the coding regions is very shortsighted, reflecting a protein chemist's bias of looking at DNA." Coding regions may make the proteins that are dear to a chemist's heart; but true biologists, he added, know that much of the exquisite control over these proteins is held offstage, nested within the noncoding junk.1994 NYT article

Some studies have found that noncoding DNA plays a vital role in the regulation of gene expression during development (Ting SJ. 1995. A binary model of repetitive DNA sequence in Caenorhabditis elegans. DNA Cell Biol. 14: 83-85.)

....(new article) The Science article reports on a paper suggesting that the non-coding 97% of the DNA, commonly referred to as junk DNA, might have a function. The authors of the paper employed linguistic tests to analyze junk DNA and discovered striking similarities to ordinary language. The scientists interpret those similarities as suggestions that there might be messages in the junk sequences, although its anyone s guess as to how the language might work. * F. Flam, Hints of a language in junk DNA, Science 266:1320, 1994.

source

But even if they hadn't, it would still seem to me it's actually enough for them to have stood by silently and wondered how it would turn out. "I don't know, let's look into more" is a right answer. "It has no purpose" is not.

Oh, I agree entirely.

Best to you.

Posted by: Ryan W. on August 4, 2009 02:42 PM

Ah, my bad! I completely misread the second source (Wikipedia). I also note it has a "citation needed" thingy next to it, which usually means something is less reliable. But, being intellectually honest (or trying), I've dug up a reference:

For bacteria with unsheathed flagella, such as E. coli, mutants with defects in genes encoding three hook-associated proteins (HAPs) are nonmotile and secrete unpolymerized flagellin subunits (66). HAP1 and HAP3 are the connector proteins that join the filament to the hook. Without the ability to adapt flagellin subunits to the hook, the flagellins are secreted. HAP2 is also called the distal capping protein because its role is one of a cap or plug. Without this cap, flagellins are also secreted. Since purified flagellin subunits can assemble in vitro and since an S. enterica serovar Typhimurium mutant lacking HAP2 can polymerize filaments if the concentration of flagellin in the external medium is high, the role of HAP2 has been viewed as capping the flagellar tip to retard subunit secretion sufficiently to increase the local concentration of flagellin and promote self-assembly. Recent work in Salmonella, analyzing cap-filament interactions by cryoelectron microscopy, suggests a model for the cap as being a flat, disklike pentameric structure that acts as a processive chaperone, preventing the loss of flagellin monomers and actively catalyzing folding and insertion into the filament.

So both are apparently true: flagellin apparently does form something into something in an artificial, pure environment, AND the cap is essential to the process in bacteria, apparently performing exactly as I'd suggested (via Pitman).

It also seems a bit of a mystery how the flagellin gets down the tube in the first place:

To reach the growing end of the filament, flagellin synthesized in the cytoplasm has to be exported though a narrow (20 Angstrom diameter) channel that runs through the core of the filament. The conformation that flagellin adopts during transport remains a mystery.... Because the channel is too narrow for folded flagellin even if domain rearrangements are possible, it has been proposed that considerable unfolding is required before export can begin.

Thanks for the correction, BTW!

I see one group of people suggesting hypotheses to try and answer this question and a second group just sitting on their hands. "We don't know" is a fine starting point, but it's only that. It's not a predictive theory.

I think I've amply defended the crucial importance of naysayers of bad theories. Again, people suspected there was something wrong with Ptolemy's model long (a century or more) before anyone was able to replace with with a similarly predictive model.

You want to hold onto a bad model because it generates specific answers? Great, vintage Marxism should be wonderful. Unlike the real world, where nobody's working hard on given the kind of Scientific Historical predictions Marx supplied. Marxists are so much better, eh?

I've also already answered your assertions about how "predictive" ID is in comparison to its exact opposite. If you'd like to engage those arguments, go ahead and take one specific one on. But I'm not going to retype them again in this particular comment box.

Further, your argument here is little more than an ad hominem argument from motives. Besides being fallacious, it also appears to be wrong, as a generalization.

Dawkins isn't out there trying to find an answer. Dawkins is interested in using certain answers for polemic reasons. Likewise, just to pick another example, Miller doesn't strike me at all as interested in the actual answer, or he'd be able to at least read the arguments his opponents are making. I'm sure some are, but it's also clear some have other motives. You yourself just admitted your professor seemed utterly closed to exploring certain possibilities. You think that's a rare exception? What suggests that? The fact that anyone agreeing to some aspect of ID, or criticizing some point of orthodoxy, can be driven from their post?

Conversely, I've pointed out that there are a lot of people who embrace ID because of work they have done, or are currently doing in research.

Look at astronomer Guillermo Gonzales. He's one of the most-cited astronomers today, and has done a tremendous amount of work on 'habitable zones' and other areas related to the formation of life on earth. His work has been featured on the cover of Scientific American. And you sit there and claim he and other ID proponents, desire to contribute nothing to our knowledge and progress, and aren't looking for answers?

Oh, and while we're at it, I'd like you to list major research being done into materialism. Really. Right now.

Simple question, Ryan, a little off topic, but I think it goes to the fallacy from which I believe you're operating: Do you believe miracles can be investigated? Seriously, if something supernatural occurred, could it be documented? How could you operate rationally in such a potential universe?

In your world, it seems to me, there's no possible way to notice such phenomenon. Either you presume, dogmatically, they can't occur in the first place, or you shoot the messenger, should someone be able (or even attempt to) to demonstrate the gross improbability of some event. Atheists complain that any alleged God has left no evidence of his existence, but then work to systematically prevent, prima facie, any discussion or evidence which they think might point to such.

The pretend-complaint is that ID proponents don't do much work on ID.* (Gee, they'd really love to know more about it, wouldn't they?) But that pose is belied by ending the careers of anyone, no matter how productive, who is suspected of being associated with ID. (Gonzales, again.)

I can see holding either view. But haven't you noticed the contradiction in pursuing both?

(* Never mind that ID is as much an "auxiliary" view as "materialism", which very much finds its way into 'science'.)

Look, I'm from computer science. In our area we have problems (like the Halting Problem) which have been demonstrated to be impossible. We don't shoot the people who try to characterize problems as such because KNOWING something is grossly improbable is benefit, not a shame. But apparently, we CS people should have been out there diligently working on a solution to the halting problem.

Don't you see? Years are wasted on stupid fads, or denying otherwise-obvious things, because the majority operates from a dogmatic materialistic point of view. When I present evidence to you, you say: "Oh, that's just a character flaw."

The problem is not the theory, per se, but the lack of humility associated with some of its advocates.

Well, the people who manifested it didn't think it was an aspect of their character. I believe they sincerely tell the truth when they say that Darwinism, as they understand it predicted junk DNA, junk RNA, junk proteins, useless vestigial organs, etc. You know them better, presumably?

This has been going on for a century now, Ryan, and it's not merely a few malfunctioning bad apples from the barrel.

That was the broken link...

The scientific literature shows a complete absence of concrete, causally detailed proposals for how coevolution and co-option might actually produce irreducibly complex biochemical systems In place of such proposals, Darwinists simply observe that because subsystems of irreducibly complex systems might be functional, any such functions could be selected by natural selection. Accordingly, selection can work on those parts and thereby form irreducibly complex systems. [Dembski]

Behe and other ID-proponents have long-acknowledged "exaptation" or "co-option" as an attempt to evolve biological complexity, and have observed many problems with "co-option" explanations. [...] one could find a sub-part that could be useful outside of the final system, and yet the total system would still face many points along an "evolutionary pathway" where it could not remain functional along "numerous, successive, slight modifications" that would be necessary for its gradual evolution. [Luskin]

What "mainstream scientists", like Kenneth Miller, don't seem to understand is that all systems of function are irreducibly complex regardless of whether or not a working subsystem can be found within the larger system. [Pitman]

I apologize for the single broken link, but each of the first three articles I linked for you contained (or we even mostly focused on) ID proponents acknowledging that sub-units of some allegedly IC component (BF, in this case) could provide some functionality. Heck, one of them was even entitled "Do Car Engines Run on Lug Nuts?"

Do IC arguments provide more details? Well, I've demonstrated that an unadorned secretory system can and does, in fact, provide the "function" of motility prior to being co-opted.

The question is how to go, stepwise, from some already-existing components to the bacterial flagellum. Mentioning that some part (not the same part mind you, but one which fits into the same category) in another cell, can provide a completely different behavior which fits roughly into the same category (motility) -- gets us what?

You're not even showing the connections.

Look, I could care less whether some of the sub-units provided motility or worked as a sort of cellular hot chocolate dispenser. What they did in their previous life no special relevance. If something provided "motility", of a completely different sort, then there is no less burden incurred.

What's missing is the steps from A to B. Talking about a similar part, in another cell, with no discussion about how to mutate it into the current form, and how many viable steps exist between the two — gives us precisely nothing. The argument something similar to one such part may be involved in (a completely different form of!) "motility" also adds nothing.

(Though I guess it's a specific nothing, which automatically imbues it with an aura of respectability.)

Dembski does not seem to address that in the section cited, but only that a subsystem of an already IC system might be functional outside of the system.

First: Dembski addressed the arguments actually being made. As I said before, he doesn't have a burden to come up with every form of argument his opponents might make, and refute them himself.

Second: In addition to what I wrote above, the fact that nobody else is making this particular argument suggests to me (no offense) it's probably not that strong.

Third: I'd note that you're also wrong about whether addressed your argument. He plainly did:

What's needed is a complete evolutionary path and not merely a possible oasis along the way. To claim otherwise is like saying we can travel by foot from Los Angeles to Tokyo because we've discovered the Hawaiian Islands. Evolutionary biology needs to do better than that.

Again, I've said the same thing too, repeatedly.

I keep explaining why I don't think "hand-waving" arguments ("something like this might have done it!") are even a form of evidence. Rather than address my objection head on, I keep hearing more hand-waving arguments. Even if I'm wrong, that's not going to be constructive, given my previous objection.

Info generation: What counts as evidence?

There's lots of possibilities. Again, why put the burden on me? If you feel you have something which is evidence, go ahead and post it. Trust me, if I think it's not really evidence, I'll be sure to say so.

But, just to be a sport: The formula for biological life would certainly count. Or, for me, an every-step viable sequence which would produce the bacterial flagellum from other components. A stochiastic system which produces meaningful information, which wasn't front-loaded, fast enough that it could explain increasing complexity in DNA. Proving that a feasible number of "monkeys with typewriters" could produce "Shakespeare" (feel free to substitute analogues for quoted terms) in a meaningful time.

Again, I'm sure there are more possibilities.

Yet I see none of these things, so I strongly suspect they don't exist.

Dawkins is conspicuosly late to the party

Hmmm... perhaps there's something about the way he looks at the world which might have contributed to that? >;-)

Posted by: Tim (Random Observations) on August 5, 2009 12:28 AM