Does ID predict genetic similarity?

A nested hierarchy incorporates both homologous and derived features.

Then show me an outboard motor designer that produces designs by heavily modifying a pump. I really doubt that any rational designer does this.

What we see in the bacterial flagellum is an evolutionary history. Liu and Ochman (2007) demonstrate that the evolutionary history of the bac flag involves gene duplication and divergence, and common ancestry with secretory systems. We can find the stepwise evolutionary history for this system.

Yes, just like a car is hollow and a boat is hollow, therefore you should start with a boat when designing a car. Sorry, it doesn't make sense.

Either way, both modern systems evolved from a common ancestral system.

Yes, just as every part of the Rube Goldberg machine plays an important part in its function.

This is the ultimate cop out for ID. They claim that if ID is true then the results should mimic evolution. Sorry, but that is not a winning argument.

Yes, but then you would expect a nested hierarchy even from machines that are originally designed because components of that machine could be co-opted by evolutionary mechanisms, producing a nested hierarchy that is primarily derived.

In short, a whole bunch of the flagellar proteins either lack any homologous counterparts or lack precursor parts. This is not what we would expect from evolution, is it?

Do you sincerely think this is a reasonable argument Taq? Our outboard motors don't have to be designed in the cell - they are designed in solid, static objects. Consider a boat for example. Since there is no need to pump parts of the outboard motor for assembling it, there is no need to build it around a pump. This is obvious, plain and simple.

I'd suggest that you not cite awful papers that mess up badly in bioinformatics. See here, here, here, here, and here. You've cited this paper before, I pointed out that it's dreadfully wrong, and now you're bringing it up again. Oh well.
Anyways, it means that we cannot, in fact, "find the stepwise evolutionary history for this system."

Perhaps that's because a flagellum isn't a car or a boat. I can only reiterate what I said before: since constructing the flagellum requires that a whole bunch of filament proteins assemble outside of the cell (because it is a motility device, after all), this presents an engineering problem. The problem is solved by embedding a pump in the basal body of the flagellum, such that the filament proteins are pumped outside of the cell membrane. This makes perfect sense. It's actually a pretty clever design.

Yes, but if the common ancestral system is none other than a bacterial flagellum, as a number of researchers have contended, then the flagellum isn't a modified secretion system, despite what you (repeatedly) say.

I find this answer most unsatisfactory. I provided a good reason for why biochemical pathways should be cascade systems.

What you're saying is that front-loading is an ultimate cop out for ID. I disagree because IMHO front-loading makes different predictions than non-teleological evolution, but we've discussed this before. Nevertheless, it is simply true that if life was front-loaded we'd expect a nested hierarchy.

Further, as I explained above, the components of a number of biological machines can't be easily placed into a nested hierarchy (unless you have them as the ancestor system, in which case there is no problem for ID).

Edited by Genomicus, : No reason given.

Edited by Genomicus, : No reason given.

I can see that you think that as you posit an argument that you don't believe to be true yourself. In my world, being a crazy idea is a very good argument against it. If you want to dream up imaginary and arbitrary scenarios and claim them to be proper arguments, I guess nothing is going to stop you, but you can expect a little push-back from the real world.

Yes, I tend to need an argument to be remotely credible before I accept it; does that seem odd to you?

The logical argument says that the ID views you've put forward all fail Ockham's tests so now you have to have to come up with some proper evidence to show why your more complex - and so far incredible ideas - are better than the current understanding.

And yet you didn't say I don't know - you came up with a whole cock-and-bull story about electric aliens.

Ok, we can kill this one. I read form this that your position was the usual one of panspermia; the obvious response to which is that if life didn't start here it still had to start somewhere; which leaves the philosophical problem of regress.

Most people jam the divine in somewhere back along that path. Sadly the ID movement is no exception - they are just more dishonest about it claiming to be disinterested and only searching after truth. It's a lie that they've been caught out on several times.

If you don't fall into this camp, then you are unique and I congratulate you on it. But you still have to support your claims with more than just thought puzzles.

Exactly.

We also see that the use of evolutionary programs for designing devices have produced successful designs that were better than human designs, so we can see that evolution can be a good tool to achieve or approach desired outcomes.

What we can't determine (at this time anyway) is what such desired outcomes may be for an Intelligent Designer ... rational intelligence? emergent gods? amusement⁽¹⁾?

Enjoy.

⁽¹⁾ also see Silly Design Institute: Let's discuss BOTH sides of the Design Controversy...

Edited by RAZD, : is

Indeed. Just like the hypothesis that evolution was designed. No predictions.

As we don't know what it is, we can only speculate on what its limitations might be.

But what are the predictions of the hypothesis that evolution on this planet (and therefore a nested hierarchy) is intelligently designed? What would this necessarily entail?

Front-loading does make testable predictions IMHO. I've discussed this before, and I have no intention of re-hashing the discussion all over again in this particular thread.

Alternatively our ID hypothesis can be built around a designer with assumed abilities, and then we can go from there with our predictions.

See here for a discussion on this (specifically, a prediction of front-loading).

Edited by Genomicus, : No reason given.

You wouldn't expect a nested hierarchy in this case. For example, humans put the jellyfish GFP gene in vertebrate fish (see Glofish). Overtime we would expect these sequences to diverge, but we would not expect this gene to suddenly appear in other species of fish. Therefore, this would be a clear violation of the nested hierarchy.

They share homology between the flagellar proteins demonstrating that the flagella was built up by gene duplications and subsequent divergence of those proteins.

quote:

---

Stepwise formation of the bacterial flagellar system.
Liu R, Ochman H.
SourceDepartment of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA.

Erratum in
Proc Natl Acad Sci U S A. 2007 Jul 3;104(27):11507.

Abstract
Elucidating the origins of complex biological structures has been one of the major challenges of evolutionary studies. The bacterial flagellum is a primary example of a complex apparatus whose origins and evolutionary history have proven difficult to reconstruct. The gene clusters encoding the components of the flagellum can include >50 genes, but these clusters vary greatly in their numbers and contents among bacterial phyla. To investigate how this diversity arose, we identified all homologs of all flagellar proteins encoded in the complete genome sequences of 41 flagellated species from 11 bacterial phyla. Based on the phylogenetic occurrence and histories of each of these proteins, we could distinguish an ancient core set of 24 structural genes that were present in the common ancestor to all Bacteria. Within a genome, many of these core genes show sequence similarity only to other flagellar core genes, indicating that they were derived from one another, and the relationships among these genes suggest the probable order in which the structural components of the bacterial flagellum arose. These results show that core components of the bacterial flagellum originated through the successive duplication and modification of a few, or perhaps even a single, precursor gene.

---

Even the criticisms agree with the meat of the argument. From your first link:

"The authors argue, as have I and others, that the flagellar axial proteins, about 10 of them, evolved by duplication and diversification from a common ancestor. But this is miles away from demonstrating that all flagellar proteins come from one gene, and in fact the extra-flagellar homologies show positively that this cannot be true, as anyone who has read the literature on this topic should know (the authors exhibit some awareness of these homologies, but they don’t seem to see the implications)."
http://www.pandasthumb.org/...2007/04/flagellum_evolu_1.html

So we still have an evolutionary history for this system, a stepwise sequence of gene duplications for at least 10 of the proteins, if not more. We also have the homologies with secretion systems.

It does not make sense since secretion pumps are not needed for other extracellular features such as pili.

Then why would a designer start with a flagellum and make a pump out of it? Either way, you are unnecessarily modifying a pre-existing system which is not what a designer does.

Rube Goldberg machines are also cascade systems with some steps amplifying the signal from the previous step.

As I have shown, front loading commits the Texas Sharpshooter fallacy. Also, designers do not front load their designs. This is also irrational design. If a designer wants a car they build a car. They don't front load a replicator and hope to get a car out at the end of it.

Yes, we would expect a nested hierarchy with the originally designed protein being at the base of the tree. And this is what we see for a number of flagellar proteins. E.g., if we designed a bacterial flagellum and put it out in the wild, over time we would expect the blind watchmaker to tinker with it and borrow its components for other uses. What would result is a nested hierarchy with the originally designed state at the root of the tree.

You mean some flagellar proteins share homology with other flagellar components. This doesn't address what I said, which was:

If the type III secretion system evolved from the flagellum, as I believe the evidence suggests, then about half of the flagellar proteins either (a) lack homologs at all or (b) lack any precursor proteins.

But that's not the meat of their argument, is it?

"The authors argue, as have I and others, that the flagellar axial proteins, about 10 of them, evolved by duplication and diversification from a common ancestor. But this is miles away from demonstrating that all flagellar proteins come from one gene, and in fact the extra-flagellar homologies show positively that this cannot be true, as anyone who has read the literature on this topic should know (the authors exhibit some awareness of these homologies, but they don’t seem to see the implications)."

Yet the Liu and Ochman paper that you cited made the strong claim that:

This is the meat of their argument, and not that the 10 or so flagellar rod proteins are homologous to each other, because this has been known for quite some time - and since this has been known for some time this obviously could not be the meat of their argument as you claim. The meat of their argument is very thoroughly shown to be wrong.

You mean we have similarities among flagellar components. We still lack a stepwise sequence of gene duplications because no accurate phylogenies for these paralogs have been constructed.

And yes, we do have homologies with the TTSS but this doesn't strengthen the case that flagella evolved if the TTSS is a descendent of the flagellar system.

Yes, but pili generally don't extend well beyond the cell surface. For example, type I pili assembly takes place in the periplasm, but this does not involve the thousands of flagellin subunits involved in the assembly of the flagellar filament. Pili are not involved in cell motility, with the exception of the type IV pili (which generate twitching motility). Yet, interestingly enough, type IV pili are built around a pump - the type II secretion system. The fact that the only pili that generate motility use a pump for assembly suggests that this is a very rational way to assemble a large number of subunits outside of the cell.

Embedding a pump in the flagellum is a very rational design because it solves the engineering problem of assembling ~20,000 FliC subunits of the flagellar filament. In fact, would you be willing to propose a more rational design for filament assembly?

Two points:

1. I don't think that the type III secretion system was designed, making your first question a moot point. It could however fit comfortably with front-loading, wherein the flagellum was poised to evolve into an export system once eukaryotes arrive on the scene. It should be noted that not all type III secretion systems are involved in disease, and from a design perspective I would predict that the original TTSS had a role beneficial to eukaryotes. This is a subject for a future post (yes, I know I've got a lot of essay ideas stacked on the table).

2. You state that "you are unnecessarily modifying a pre-existing system which is not what a designer does." This is plainly incorrect. Engineers very often modify pre-existing systems.

For example, this quote comes from a Hunt Engineering article:

"We use a modular approach wherever possible so that we can re-use technology that we develop in a very wide variety of systems. All of our modular products are designed to be as flexible as possible so that they might address the needs of many different customers."

From "Structural studies and protein engineering of inositol phosphate multikinase":

Here we report the structure of Arabidopsis thaliana IPMKα at 2.9 angstrom and find it is similar to the yeast homolog Ipk2, despite 17% sequence identity, as well as the active-site architecture of human IP3 3-kinase. Structural comparison and substrate modeling were used to identify a putative basis for IPMK selectivity. To test this model, we re-engineered binding site residues predicted to have restricted substrate specificity. Using steady-state kinetics and in vivo metabolic labeling studies in modified yeast strains, we observed that K117W and K117W:K121W mutants exhibited nearly normal 6-kinase function but harbored significantly reduced 3-kinase activity. These mutants complemented conditional nutritional growth defects observed in ipmk null yeast and, remarkably, suppressed lethality observed in ipmk null flies. Our data are consistent with the hypothesis that IPMK 6-kinase activity and production of I(1,4,5,6)P4 are critical for cellular signaling. Overall, our studies provide new insights into the structure and function of IPMK and utilize a synthetic biological approach to redesign inositol phosphate signaling pathways.

Also see here, here, here, here, here, and here. Finally, just do a Google search like this.

Do you really want to argue that engineers don't modify pre-existing systems?

But in the non-biochemical world such systems aren't needed. To take the example of the toothpaste, we could easily just squeeze the stuff out. Not so in the biological world. If you have a stimulus for which you need a rapid reaction, you'll need a cascade system. Consider blood clotting. If you remove most of the proteins in the cascade system, will you have efficient blood clotting? Not at all. So what do you think a better system would be?

Cascade systems are a pretty good idea when it comes to the cell.

If life is front-loaded, then we expect a nested hierarchy. I don't think you dispute that.

Having said that, there are good reasons for front-loading a design: e.g., directly designing animals, for example, on the early hostile earth is not a good idea, is it? It would be better to design the first cells such that they are likely to evolve into animals.

Edited by Genomicus, : No reason given.

Edited by Genomicus, : No reason given.

I remember the thread, which was where I pointed out to others that you hadn't strayed from naturalism in the implications of your posts at that point.

But I didn't agree that your specific hypothesis made the predictions you claimed. And I thought that there were other more plausible front loading hypotheses.

On this thread, I think that the phrase "rational design" is problematic, and requires a rigorous definition if it's to be useful.

Could the kind of rock arch called a "natural bridge" be said to exhibit rational design if it functioned perfectly as a means by which animals could cross from A to B avoiding a gully and/or stream? If not, why not?

And could the water cycle, which has an essential function for larger land organisms, be said to exhibit rational design?

The common reason for the idea of a perfect creation is that there was no death before Adam's sin, which occurred about 6,000 years ago. I cannot at all reconcile this view with the evidence. Whether it was at one time a perfect world, one can only guess, but it seems that the world has pretty much been operating in pretty much the same way for a long, long time.

An acceptable answer, IMHO, to which I can agree. The trouble is that science deals with natural events and natural processes, so coming up with a procedure intended for natural processes to detect non-natural events is very problematic, to say the least.

HBD

I didn't miss your point. You asked why would a designer be bound to using principals. That is what I responded to. A designer would be bound to using principals within a physical universe. How else could it function?

You seem to suggest that because a designer could design in any way he wanted that we cannot use observations to formulate a hypothesis. Not so. The principals of the physical world are not predictions of the ToE either, even though they are a requirement of evolution. I say that principals are a requirement of a designer also.

I agree that that the principals that govern the universe are not a prediction of an intelligent design hypothesis, but for a different reason. They cannot be tested and falsified. We can't test a universe with no principals or exclude certain ones. Principals are just that, principals. A designer would be bound to use them. Not necessarily the ones we observe, but principals none-the-less.

HBD

You did miss my point. I asked GDR:

I was referring to a hypothetical designer of worlds and principles, not one which is constrained by this physical universe.

That there are principles and that we are in a physical universe are observations, not predictions of the hypothesis "an intelligent designer made the world".

You may say it, but unless you can demonstrate that your designer is constrained to design only worlds with principles, you'll just be making an unsupported claim. What or who constrains your designer?

Principles. Again, you can't support your last two sentences, yet you want to state "a designer would be bound to use them [principles]" as if it's a fact, after having seemed to agree that principles are not a prediction of an I.D. hypothesis.

My first post under this subtitle was one in which I was laughing at people who would consider both the breaking or absence of principles (miracles) and the principles themselves as evidence for a supreme intelligent designer.

It's surprising how many theists do actually think like that.

So I said: "Make up your minds."

Let me see if I can help:

It is logical that whatever universe the designer/s made, that it would have principles put in place that govern how it operated on a mundane day-to-day basis. What anyone within that universe observed would then be the principles established for that universe to operate, as established in the process of creating it.

Agreed ... of what was (possibly) created ... and it is perfectly logical to assume that such observe principles would therefore be part of that particular universe creation process.

Again, I agree with you there. ... it is more of a philosophical hypothesis than a prediction of a theory.

But then I don't think ID as currently used, or as it should properly be used (in philosophy rather than science), can make scientific predictions (my personal opinion).

This is also waay off topic regarding genetic similarity ...............

Enjoy.

Edited by RAZD, : clrty

Edited by RAZD, : ..

This is a troubling problem indeed, but is the only convincing evidence of a designer a perfect world with no death or trouble? This is a physical universe, subject to decay and strife. I don't claim to understand why. But do you think that a perfect world without death and suffering is the prediction of an ID hypothesis?

Yes, but aren't there numerous connections off the RLN? It's more like running the extension cord across the livingroom and plugging in a lamp, a clock , looping it behind the couch, plugging in a heating pad, then back to the tv even though the plug is right by the tv. Poor design? Yea, sure, I wouldn't do it.

But don't you think this is problematic for the ToE also? Both the length of the RLN and the length of the neck need to coincide during development. As the neck vertebra get longer, so the RLN gets longer. Are the vertebra and the RLN controlled by the same genes and the same developmental pathway? For example, as the giraffe's neck gradually became longer, ie. the vertebra became longer, the RLN could stay basically the same length, no longer loop around the aorta but still make an "unnecessary" loop.

from Message 82

Well it sure makes learning biochemistry a nightmare! But wouldn't a designer need to program in redundant fail-safe systems to prevent unwanted PCD? There are also several pathways to regulate the process under different conditions and for different situations. There are also cascades that control expression and offer another level of regulation. Hardly a toothpaste dispenser. Could you come up with a simpler, more efficient design? Probably. Would it work as effectively in all conditions? Uncertain.

The discussion on this thread seems to be centered around whether intelligent design is even a legitimate question to pursue in the first place. Let's assume it is, since the reasons for asking the question in the first place are philosophical and that's not what I wanted to discuss.

This is what I want to NOT do. I think genomicus is also trying hard to take a positive approach to this as well. Whether you agree with his conclusions or his predictions, you should agree that he is trying to make testable predictions based on his philosophical ideal. That type of work should be embraced, even by those who are skeptical of an intelligent designer, as it could lead to new understanding of our world.

What would you predict a material world that was operating WITH supernatural influence would appear like?

HBD

I did open it up to allow other predictions that ID makes or could make. I didn't want a deeply philosophical discussion, but it seems the question is considered illegitimate to begin with. You can't make predictions if you can't ask the question.

I guess where I personally am stuck at on this subject, is that I feel there should be an overlap, a place where philosophy and science interact. Do you feel philosophy and science are two completely independent ideals or that scientific observation is sufficient to support philosophy but philosophy is just unable to make scientific predictions?

HBD