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  Topic: more flag refs, the old thread seems stuck< Next Oldest | Next Newest >  

Posts: 319
Joined: May 2002

(Permalink) Posted: June 05 2003,20:00   

New ISCID thread:

The main "problem" with Smart's paper is basically that, with such a clear grasp of the definition vs. evolvability distinction, and of the various complexities of biology that have to be taken into account when defining multiple-parts-required systems (which is basically what he boils the concept down to), he really should just come on over to the evolutionist side and conceed that IC is not the forbidding barrier to evolution that it has so often been claimed to be!

I shall outline the reasons why:

1) The "varying required parts" problem
Smart explicitly acknowledges (in a way that I don't recall other IDists doing, certainly not emphasizing -- he sort of says that Julie Thomas did this, but as far as I can recall she looked at "parts present in multiple organisms" vs. "parts found to be required in multiple organisms") the common biological fact that homologous multiple-parts required systems with the same function, often have parts that are required in one system, but not in another!  As RBH points out, unless one is going to invoke a multitude of mini-ID events for each of these "extra" required proteins in various systems (Hagemann factor is an example, it is at least very important in humans (defects are associated with miscarriages etc.) but in whales it is just a pseudogene), then the "IC barrier" has already been breached, probably by the "incremental indispensability" argument.

2) If you take a "concessionary" viewpoint, then even for the famous ID systems not much is left of the IC systems
For example, for the flagellum, Smart lists the following universally present proteins:


[note: I am making a few changes based on how I would describe the parts; this is just rearranging, it doesn't lower the parts count]

Cap: FliD
Filament: fliC [/flaA/flaB*]
Hook: flgE [hook cap: flgD?]
Adaptors: flgK, [flgL?]
Drive shaft: flgB, flgC, [/flgF?]
Motor complex: motA,motB
[Rotor "teeth" -- interact with MotA: FliG]
[Rotor/T3SS base ring: FliF]
Export machinery: flhA,flhB, fliR, fliQ, fliP,, fliI, [double comma there BTW]

Unknown fliS - essential, but function unknown
flhF - GTP-binding protein
But, if we follow the concessionary approach, we have in the T3SS homologs of:

[Rotor "teeth" -- interact with MotA: FliG]
[Rotor/T3SS base ring: FliF]
Export machinery: flhA,flhB, fliR, fliQ, fliP,, fliI, [double comma there BTW]
In the ExbB/D family we have homologs of:
Motor complex: motA,motB

Cap: FliD
Filament: fliC [/flaA/flaB*]
Hook: flgE [hook cap: flgD?]
Adaptors: flgK, [flgL?]
Drive shaft: flgB, flgC, [/flgF?]
...and, the interesting thing about this group of proteins includes:

(1) the apparent repetition of the filament-cap system in the hook-hook cap system

(2) sequence and structural similarities between the various rod and hook proteins (and FlgK/HAP1 I think)

(3) similarities between FliC, other filament proteins (some flagella have 6+ filament proteins), and (IIRC) FlgL/Hap3

(4) hook-type III pili extension homologies proposed in recent articles

...which all seems to point towards the potential of all of these proteins being modified copies of each other (many of them are already in the "axial protein family".  

The cap proteins are not quite so clearly required parts anyhow:

- it appears that Type III pili might not have them
- flagellar filament protein will spontaneously assemble in certain conditions
- and null mutants for cap proteins are still functional e.g. in bacterial with sheathed flagella (the sheath, an extension of the membrane surrounding the flagellum, apparently concentrates the filament protein enough that it assembles without the cap)

And the cap proteins might even be modified axial family proteins themselves -- e.g., the cap-filament interactions are similar to filament-filament interactions; it takes about 5 filament proteins to complete a turn of filament, and the cap is a pentamer of cap protein.

(some refs for the above are here)

So basically, the mighty flagellum has been boiled down to 3 "parts", corresponding to:

1. A secretion system (BTW, Smart calls it an "excretion" system -- this is probably not the best term IMO :-) ).  Secretion systems are ubiquitous functional structures in life.

2. A extracellular extension (secretion system + extension = pili).  Pili are ubiquitous functional structures in life.

3. A stator/motor, which just happens to independently associate with the rest of the structure, and just happens to have phylogenetically widespread homologs that function in much simpler contexts.

...each of which are functional in nonflagellar contexts.

Now, we've left out the chemotaxis system and various other details:

(I suspect that FliG is more likely derived from the complement of the MotA/ExbB system rather than having been on a primitive T3SS; chemotaxis has been left out entirely but it is highly variable and not required for functions such as dispersal or even biofilm formation), and Julie Thomas/Josh Smart leave them out anyhow; discussing all of the chaperones etc. would require much more knowledge about what they and their homologs are, plus Smart leaves them out; the origins of a primitive T3SS have not been explained this is a different question, and the detailed functions of the parts are not even well-understood yet; etc.)

...but certainly the "big picture" is that the "unscalable cliffs" of this IC system seem much reduced.

3) Inconsistency in detail requirements

Smart writes, "Critical responses to irreducible complexity have primarily consisted of just-so-stories that substitute vague appeals to chance or other forces for well-thought-out counter-arguments." And actually, I think that there is some truth to this.  You can go through the book reviews of Behe and find that very few do more than vague just-so stories.  Part of the reason is that detailed discussions are impossible in book reviews, but much of it is that the various philosophers and organismal biologists that replied simply didn't know much about the relevant biochemistry.  There were a few exceptions, e.g. Cavalier-Smith (1997, TREE) cited a half-dozen of his own 30-page-plus papers on the origin of life and various systems, work which has continued in a massive fashion to the present day (do a PubMed search on Cavalier-Smith).

However, if Smart is really looking for details, I recommend that Smart instead read the literature on the best-explored of Behe's original IC systems, the immune system.  A good introduction is this article:

Evolving Immunity
A Response to Chapter 6 of Darwin's Black Box

...and particularly the various forms of conceptual flailing that resulted among the IDists on the various ISCID threads discussing it: ISCID immune thread 1, ISCID immune thread 2.  (There is also an AE thread with many of the important links etc.)

When presented with detail and peer-reviewed literature on the evolution of this IC system, the IDist response was incoherant.  So until someone like Smart delves into this literature and really grapples with it, and explains what exactly the IC system is and what all of these organisms with progressively simpler-yet-functional systems are doing, and how all of these evolutionary hypotheses have been proposed and tested in the field of evolutionary immunology when evolution didn't actually happen, all claims about evolutionists lacking in detail will be unimpressive.

Finally, when Smart wrote, "Critical responses to irreducible complexity have primarily consisted of just-so-stories that substitute vague appeals to chance or other forces for well-thought-out counter-arguments" did it not occur to him that this is exactly what ID does?  What is "IDdidit" except the vaguest just-so story ever told?

Smart, unlike any other ID sympathizer that I can recall, actually does come up with a reasonable notion of what "detailed" should mean:


It is not true, as has been claimed, that intelligent design theorists hold any system that has not been given a detailed evolutionary explanation as something that cannot be produced by evolution (see, for example, [5]).

[BTW, does someone recall where Dembski said essentially the opposite of Smart on this point; it was right here on ISCID]

It is true, though, that there has been no detailed evolutionary explanation given for any irreducibly complex structure.

[again, see the immune system and re-evaluate]

A detailed evolutionary explanation does not mean that every base pair and selective pressure involved in the production of the system be accounted for, and every mutation explicitly stated on a timeline. On the other hand it does mean accounting for changes in phenotypes, and the advantages that those changes give.
This final criterion for detail seems quite fair.  I think that such things have been acheived for e.g. the immune system and the Krebs cycle.  They are clearly constructable for the flagellum, although our evidence is much sparser there.  However, what is the comparable standard of detail for an ID hypothesis?  There must be some detail, or else nothing is ruled in or out by the hypothesis, and it becomes nonexplanatory and nontestable.

4) Is the Avida experiment which I'm sure RBH will discuss sufficiently.  My only point would be that Smart's endorsement of the knock-out criterion would appear to clearly rule "in" the evolved EQU functions as IC.

That's probably enough for the moment.  I'm not sure if Smart himself has any interest in the discussion, but if he does, I'd like to say thanks for an interesting article, and that if he follows his logic just a very few steps further he will have one of the more thorough Behe rebuttals out there.  :)

  19 replies since June 04 2003,02:48 < Next Oldest | Next Newest >  


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