A question about IC

Most of your questions will probably be answered here:

http://www.overwhelmingevidence.com/oe/node/362

BTW, just coming up with a model does not mean such an event could reasonably occur. Let's say you have a scrapyard and monkeys are randomly taking pieces (which might be IC in themselves) and recombining them. Objects that don't function get junked by the monkey owners. So if we wanted a bike Directly ALL of the pieces involved would have to come together at once, since a partially completed object can't serve as a "standard bike".

Here's an analogy of an Indirect pathway for a bike. A unicycle, not a standard bike, comes together via a chance arrangement of wheel, nuts/bolts, tire, seat, and pedal. So it's functional and won't be junked. But the reason this pathway is Indirect is because although the unicycle is useful and functional it still isn't a standard bike. So then by chance the frame is modified and a duplication event creates another wheel. Homologous structures like chains, gears, and handle bars are found on other objects tossed into the monkey junkyard. The monkey co-opt these features for use in their standard bike. So we have a model for how monkeys randomly put this standard bike together. But can we reasonably expect such an unlikely scenario to occur? Never mind that all the independent parts themselves require intelligence to create in the first place.

Also, the T3SS would be like the unicycle and the flagellum like the standard bike in the analogy.

What if some steps involved simplification - e.g. a component is lost, broken or simplified compared to a previous state in the pathway?

ID proponents typically have no problem with destructive modifications that help an organism/creature under particular circumstances. We just do not see evidence for major constructive creative evolution via Darwinian processes (intelligent evolution is another matter).

Darwinists usually try to argue that the T3SS predated the flagellum, but it's more generally accepted that the flagellum came before the T3SS. Why?

The flagellum appears on bacteria that are widely presumed to predate anything with a T3SS.

The gist of it is that the T3SS appears on small number of bacteria that prey on eukaryotes. It’s a weapon used to inject toxins into the prey. In the meantime the flagellum appears on a large number of bacteria that don’t prey on eukaryotes. Thus saying that the T3SS predates the flagellum is like saying that anti-aircraft missiles predate aircraft. Non sequitur. Flagella were useful to bacteria before eukarotes appeared but a t3ss would be useless before then. The prey must precede the predator.

The reasonable conclusion is that the T3SS destructively evolved (simplified for another usage) from the flagellum rather than the flagellum evolving from the T3SS. This scenario, which actually makes sense in the context of a tree of life beginning with bacteria, is also congruent with what we actually observe in nature today - useful things devolving from something more complex. Behe gives many examples of useful destructive evolution in his recent book “The Edge of Evolution”.

Yes, so given a bicycle the monkies (evolution) could make a unicycle by randomly smashing bits together but they could never assemble a tandem. The reason is that it's much less likely.

The main point is that the unicycle is an island for minimal functionality. The parts that compose the final product can't really do anything in themselves (yes...I'm sure there are OTHER creative functional uses for tires, but I hope you get the point). The monkeys may never create a unicycle in the first place, never mind the full tandem.

Now from any island there may be some gradual modifications. Envision this island being surrounded by shark-infested water. In the distance is the island for the tandem bike. How to reach it? There are many stepping stones. But some stepping stones crumble when you step on them, an analogy for modifications that have negative selective pressure. For example, if the monkeys added an anchor to the unicycle that'd be a crumbling stepping stone. The question is...is there a series of stepping stones leading to the other island?

For example, for a minimal unicycle you really don't need a seat (although it obviously helps). You could even add a horn or other relatively minor features. You could even add stickers onto the bike, which serves as an analogy to "neutral mutations" since the stickers don't help or hinder the functionality of the unicycle. But to get the full tandem bike requires several modifications in order to reach that new island of functionality. An extension to the frame throws the balance off. An extra wheel does nothing without an extended frame to attach to...never mind handle bars to steer (which are themselves useless without the other parts). Gears just add weights. A chain is useless without gears and the pedals being moved to the extension of the frame.

Now a Darwinist might be able to sit down and conceive a series of unicycles that'd evolve into a functional tandem bike. But I'd imagine they'd be barely ridable. Remember, these modifications must either aid the functionality of the unicycle. If you were to start tacking on features relevant to the tandem bike it would not help. Darwinian processes don't know of a future goal. All they know is that these additional features are causing negative selection pressure until the final goal is reached.

What about scales and feathers? I remember in biology class my teacher claimed that bird's feathers are homologous to reptilian scales. Can we make an argument that rather than feathers evolving from scales, the reptilian scales de-volved from feathers.

You're not the only one to think that:

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=557315

The strong similarities between the two peptide structures for feather and scale in the homologous regions suggests a similar conformation within the protein filaments. A likely consequence is that the additional repeat region of the scale protein is located externally to the core filament. Tissue-specific features of filament aggregation may be attributable to this one striking sequence difference between the constituent proteins. It is believed that the genes share a common ancestry and that feather-like keratin genes may have evolved from a scale keratin gene by a single deletion event.

But that concept is well over 20 years old and our knowledge of genomics has increased tremendously in that timeframe. So the changes required are unlikely to be that simple. I would suggest

A more recent overview of issues related to the "scales to feathers" hypothesis:

http://www.blackwell-synergy.com/doi/pdf/10.1046/j.1420-9101.1996.9020131.x?cookieSet=1

A website critical of this hypothesis:

http://www.evolutiondeceit.com/chapter7.php

Even among Darwinists there are people opposing the "dinosaur to bird" hypothesis.

Anyway, I don't hold a solid opinion on these hypotheses, but I would recommend reading up on the structural differences between scales and features. Especially the differences at a genetic level (don't ignore the regulatory factors, where the majority of differences are likely located).

For example supposing the neo-darwinists had identified a potential evolutionary pathway made of a series of plausible tiny genetic changes? Supposing they were able to identify a number of structures which could are likely to be homologous to the transitional structures. Would that cast doubt on my claim that X-structure is IC?

Being IC does NOT equate to "X-structure cannot evolve in principle". IC primarily deals with DIRECT Darwinian Pathways and always has. Behe has always stated that INDIRECT Darwinian pathways are another matter. Also, what is "plausible" is usually tied into positive selection pressure. Every single indirect gradual genetic change must be positively selected, which is what I highlighted with the bike example. Essentially, there must be islands of functionality that are within leaping distance of each other (or only have 1 or 2 or 3 stepping stones to connect them). So, yes, there will be some IC structures where an indirect pathway is plausible. Unfortunately for Darwinists, the flagellum is not one of them.

* If something is IC then it could only have come about as some kind of indirect evolution (e.g. using co-option or and not simply adding complexity at each step).

That's closest, but this question should be kept in mind: "where did the co-opted structures come from?" For example, the T3SS is IC in itself for a different function (and don't forget that the most likely historical narrative calls for the flagellum existing BEFORE the T3SS).

http://www.nature.com/nrmicro/journal/v4/n10/fig_tab/nrmicro1493_T1.html

The flagellum consists of 42 proteins. 23 proteins are “thought to be” indispensable in modern flagella. Out of those 23, 2 are unique. Otherwise 15 other proteins are unique. So that’s 17 unique proteins with no known homologs. So in the last couple years 13 additional homologs have been found.

But before accepting those numbers note the sequence similarities. 14 of these homologs were found by BLASTing on non-default settings according to Matzke. Whether that should be considered acceptable I can’t say. So perhaps it’s debatable exactly how homologous/unique some of these proteins truly are (never mind Behe’s work on protein binding sites). And unless I’m misunderstanding something this chart doesn’t include all of the controlling mechanisms separate from the flagellum itself. Lastly, it's possible some additional homologs have been found since Oct. 06.

The other thing to keep in mind is Design reuse (sometimes called common design) and front-loading scenarios. So we should expect a large amount of homologous structures (historical note: Darwinists used to predict that the genetic code of all creatures would be unique). This of course becomes a problem for Darwinists if homologous components are found in creatures that are not supposed to be related usually due to geographic distance/isolation. Usually their response is to claim "convergent evolution" or "lateral gene transfer" as a magic wand. Looks like a good follow up to Behe’s Edge of Evolution would be to try and estimate the limitations of lateral gene transfer and endosymbiosis from experimental data (IS there ANY data on what they’re capable of at a macro scale?).