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Author Topic:   Does ID predict genetic similarity?
Genomicus
Member (Idle past 1215 days)
Posts: 852
Joined: 02-15-2012


Message 77 of 167 (670653)
08-16-2012 8:05 PM
Reply to: Message 75 by Tangle
08-16-2012 7:59 PM


The ToE predicts both good and bad design. You have to explain the bad.

A different way of wording this would be: the ToE makes no predictions regarding the optimality or lack thereof in biological systems.

Edited by Genomicus, : No reason given.


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Genomicus
Member (Idle past 1215 days)
Posts: 852
Joined: 02-15-2012


Message 81 of 167 (670657)
08-16-2012 8:46 PM
Reply to: Message 80 by Taq
08-16-2012 8:27 PM


Since ID is based on the idea of a design process that starts with a goal then we would expect to see optimal designs. Evolution is quite different. Evolution is an ad hoc designer that can't see what it's doing, other than by looking to see if random changes improve fitness. Evolution would predict that designs, optimal or not, are modified versions of the designs seen in ancestors. ID would predict that designs would make sense in relation to function and design principles. Evolution wins, hands down.

I wouldn't be so quick to say that (non-teleological) evolution wins, hands down. There are a great many biological systems that display the properties of rational design, consistent with ID. For example, there is no molecular version of the inverted retina in the core bacterial flagellar structure. When you look to the molecular world, there are many examples of machines that could have easily been inherently flawed in their design, based on the non-teleological position, but they are not. Rather, they operate with remarkable efficiency, the arrangement of their parts is optimal, etc. - all hallmarks of rational engineering.

In a future post (and possibly in this thread - we'll see) I intend to argue that this rational design of protein machines in the cell is difficult to explain from a Darwinian perspective.


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Genomicus
Member (Idle past 1215 days)
Posts: 852
Joined: 02-15-2012


Message 83 of 167 (670661)
08-16-2012 10:17 PM
Reply to: Message 79 by Coyote
08-16-2012 8:25 PM


Re: Rational design and non-design
I've posted this several times before, but have yet to have a creationist or IDer respond with a discussion of the details.

I may or may not get around to watching the lecture, but for the moment, suffice it to say that if a biological system/network is not directly designed, there is no particular reason to expect rational design. Your example only works for those individuals who like to claim that pretty much everything was directly engineered.


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Genomicus
Member (Idle past 1215 days)
Posts: 852
Joined: 02-15-2012


Message 84 of 167 (670666)
08-16-2012 11:20 PM
Reply to: Message 82 by Taq
08-16-2012 9:00 PM


Those systems fall into a nested hierarchy which refutes the entire "rational design" argument.

This is a pretty bold claim, and I disagree for two reasons:

1. Some of these systems do not, in fact, conform to a nested hierarchy. Subsystems of the complex might share homology to other systems, but the system as a whole does not fall into a nested hierarchy since some of its component parts lack homologous counterparts. Consider the bacterial flagellum. Does it fall into a nested hierarchy? Some of its components do, but at the same time it has a number of either (a) entirely unique parts, or (b) parts which only have homologs in systems that postdate it.

2. Some of these machines may fall into nested hierarchies, but this does not "refute" the rational design argument precisely because if these machines were front-loaded we would expect them to be part of a nested hierarchy.

However, there is the fish-to-tetrapod feature in flagella. The flagella is a modified secretion system. A rational designer would not start with a pump when designing an outboard propeller, and yet that is exactly what we see.

This argument lacks rigor to a very high degree. Let's take a look at it in more depth:

1. An engineer is not forced to always use new parts. In human experience, engineers very often borrow parts from other systems and incorporate them into another system. This is not considered irrational design at all, so there is no reasonable support at all for the statement that "a rational designer would not start with a pump when designing an outboard propeller."

Furthermore, when we take into consideration the workings of the flagellum, it makes sense that the flagellum is built around a secretion system. In other words, assuming that the flagellum is in fact a modified secretion system (but see point 2), there is a good engineering reason for this. Since the flagellar filament is external to the cell membrane, this poses an engineering problem: namely, how can we design the flagellum such that a large number of proteins assemble outside the cell? This problem is solved by embedding secretion machinery within the flagellar basal body, and by making the flagellum a hollow structure. Thus, the flagellar filament can be constructed from the bottom up. It would make perfect sense to take an already-existing secretion system and attach the necessary parts such that it now functions as a motility device that can neatly be constructed by the cell.

2. You've brought up the argument before that the flagellum is a modified secretion machine, having evolved from the type III secretion system. However, there is the very real possibility - and I've pointed this out before with references to the literature - that the type III secretion system evolved from the flagellum. The two competing hypotheses are (a) the TTSS and flagellar system share a common ancestor, and (b) the TTSS evolved from the flagellum. The papers are split about evenly on the subject, but I personally find the evidence in favor of (b) to be more compelling (particularly since we know of an actual example of a secretion system evolving from bacterial flagella, namely, the Buchnera homolog of the flagellar system).

I strongly disagree. Even Behe admits that biological systems can best be described as Rube Goldberg mechanisms [note: Behe states that some biological systems (i.e., biochemical cascades) are best described as Rube Goldberg mechanisms]. When you look at the molecular world you see the equivalent of this toothpaste dispenser...Here are cellular apoptosis pathways...

You haven't explained what's wrong with the apoptosis pathway. I'm pretty sure each of those proteins play a very useful role in that pathway. Such pathways benefit from cascades so that any stimulus is amplified to an effective degree.

As Kenneth Miller explains (regarding the blood clotting cascade):

"It sure does look pretty, but why a cascade? Why couldn't we have a simpler pathway, like the lobster, where something like tissue factor activated clotting directly? Well, we could, but a complex pathway, even if it drives biochemistry students to distraction, has advantages of its own. For one thing, the multiple steps of the cascade amplify the signal from that first stimulus. If a single active molecule of Factor XII could activate, say, 20 or 30 molecules of Factor XI, then each level of the cascade would multiply the effects of a starting signal. Put 5 or 6 steps in the cascade, and you've amplified a biochemical signal more than a million times. Clotting with fewer steps would still work, but it would take longer to produce a substantial clot, and would be much less responsive to smaller injuries."

The same holds for other biochemical cascades, such as the apoptosis pathway.

I hope you also explain why a designer would be limited to a nested hierarchy.

A designer is not limited to a nested hierarchy, unless the designer is designing through evolution.

Edited by Genomicus, : No reason given.

Edited by Genomicus, : No reason given.

Edited by Genomicus, : No reason given.


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Genomicus
Member (Idle past 1215 days)
Posts: 852
Joined: 02-15-2012


Message 88 of 167 (670688)
08-17-2012 10:08 AM
Reply to: Message 85 by Coyote
08-17-2012 1:09 AM


Re: Rational design and non-design
The feedback system of natural selection does a pretty good job, eh?

Not always. Sometimes it produces sloppy stuff.

Edited by Genomicus, : No reason given.


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Genomicus
Member (Idle past 1215 days)
Posts: 852
Joined: 02-15-2012


(1)
Message 89 of 167 (670689)
08-17-2012 10:10 AM
Reply to: Message 86 by bluegenes
08-17-2012 3:45 AM


An intelligent designer isn't limited to anything, is it? So, we can easily answer the question in the O.P. title...

I already explained that ID is so loosely defined that it does not make any real predictions. Nevertheless, ID hypotheses do make testable predictions.

So, the statement "our biosphere was intelligently designed" is so vague that it obviously cannot make any predictions.

By the way, a designer is limited by its building materials (unless it is supernatural). Designers have limits too, ya know. Furthermore, if a designer is designing through evolution, then of course we'll see a nested hierarchy.


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Genomicus
Member (Idle past 1215 days)
Posts: 852
Joined: 02-15-2012


Message 90 of 167 (670690)
08-17-2012 10:30 AM
Reply to: Message 87 by Tangle
08-17-2012 4:43 AM


This is pure Alice in Wonderland stuff. Inorder to argue for ID without a deity, you have to present an idea that you don't even believe yourself - presumably because you know it to be as daft as I do.

I'm afraid that the craziness of an idea is not, in itself, an argument against it. Your main concern with the idea is not based on logic but on personal incredulity. Why don't I believe in the idea? Precisely because I have no beliefs regarding who the designer might be. I find the answer "I don't know" perfectly satisfactory when the question "who designed the designer?" is asked.

The argument is also totally redundant, given that we already have a stronger hypothesis for how life started here and a fully confirmed theory for how it went on from that point.

You're completely ignoring my point. Let's go through this again.

I said:

As soon as you step into the question of a why a divine designer would have any bad designs, you have left the realm of science and entered that of theology.

Given that it is not my position that a god designed features of life, your objection is not particularly relevant for me.

You responded:

I'm afraid you are always going to be pushed back into philosophy because saying that the design for life was not divine begs the question of how the non-divine creator came about.

In other words, you argued that if we argue from an ID position that says abiogenesis is implausible, then we will ultimately be pushed back into philosophy "because saying that the design for life was not divine begs the question of how the non-divine creator came about." This is the argument I am responding to, irrespective of whether abiogenesis is a sufficient explanation for the origin of life on earth. Through a simple thought experiment I illustrated how ID does not necessarily have to trace back to a god. This is the point of my argument.


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Genomicus
Member (Idle past 1215 days)
Posts: 852
Joined: 02-15-2012


Message 92 of 167 (670695)
08-17-2012 11:10 AM
Reply to: Message 91 by Taq
08-17-2012 10:42 AM


A nested hierarchy incorporates both homologous and derived features.

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?

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

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.

What we see in the bacterial flagellum is an evolutionary history. Liu and Ochman (2007)...

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."

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.

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.

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

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.

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

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

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.

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.


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Genomicus
Member (Idle past 1215 days)
Posts: 852
Joined: 02-15-2012


Message 96 of 167 (670722)
08-17-2012 3:18 PM
Reply to: Message 95 by bluegenes
08-17-2012 2:55 PM


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

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.

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

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

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?

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

Edited by Genomicus, : No reason given.


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Genomicus
Member (Idle past 1215 days)
Posts: 852
Joined: 02-15-2012


Message 98 of 167 (670734)
08-17-2012 9:00 PM
Reply to: Message 97 by Taq
08-17-2012 3:32 PM


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.

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.

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

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

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?

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.

Even the criticisms agree with the meat of the argument.

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:

The origins of complex organs and organelles, such as the bacterial flagellum and the metazoan eye, have often been subjects of conjecture and speculation because each such structure requires the interaction and integration of numerous components for its proper function, and intermediate forms are seldom operative or observed. However, the analysis of biological complexity has changed with the application both of genetic procedures that serve to identify the contribution of individual genes to a phenotype and of comparative sequence analyses that can elucidate the evolutionary and functional relationships among genes that occur in all life-forms. As with the evolution of other complex structures and processes (29–32), we have shown the bacterial flagellum too originated from “so simple a beginning,” in this case, a single gene that underwent successive duplications and subsequent diversification during the early evolution of Bacteria.

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.

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.

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.

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

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?

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.

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?

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

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.

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.

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.


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Genomicus
Member (Idle past 1215 days)
Posts: 852
Joined: 02-15-2012


(2)
Message 154 of 167 (672043)
09-02-2012 12:27 PM
Reply to: Message 127 by herebedragons
08-21-2012 9:25 PM


Re: Does ID predict genetic similarity?
Apologies for the belated response. I thought this thread had died, only to find that you had responded to my posts.

In the first place, ID as a concept is so loosely defined that one cannot say what it predicts at all.

While the global concept of ID doesn't make any true predictions, specific ID hypotheses do make testable predictions. For example, the ID hypothesis that "irreducible complexity can only arise through intelligent intervention" is quite testable. The hypothesis would predict that there are no non-teleological pathways to IC systems.

Conclusion:
Before we can make any statement about what ID predicts, ID as a scientific hypothesis must first be adequately defined.

This is probably one of the biggest reasons why I have not personally been able to support or "buy into" the ID movement. A specific, unified and cohesive hypothesis that can be tested and modified would go a long way to gaining support of the scientific community. However, it doesn't appear to be forthcoming at the moment.

Although I am an ID proponent, I do not consider myself part of the ID "movement" - that is, the movement that is associated with the Discovery Institute etc. One of the reasons for this is that the present ID movement is more concerned with disproving Darwinian evolution than with presenting testable ID hypotheses. Another reason is that the ID movement has undeniable religious underpinnings. We often see Evolution News and Views discussing religious topics. But if this is supposed to be about biology, then I'd expect all discussion to revolve around biology. Fortunately, there are subtle signs of this changing within the ID movement. Recently, Sal Cordova over at Uncommon Descent wrote an article that heavily criticized YEC folks like Kent Hovind. And Cordova also wrote an article at UD that critiqued the argument that the 2nd Law of Thermodynamics disproves evolution (interestingly, in both of these articles, he was heavily criticized by numerous commentators).

Still, the changes within the ID movement are slow. Thus, I encourage anyone who has an interest in developing ID as a rigorous biological hypothesis to be an independent thinker, and not tied down to the ID movement.

Edited by Genomicus, : No reason given.


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Genomicus
Member (Idle past 1215 days)
Posts: 852
Joined: 02-15-2012


Message 155 of 167 (672045)
09-02-2012 12:39 PM
Reply to: Message 128 by herebedragons
08-21-2012 9:52 PM


But ultimately the argument would lead back to some type of non-created, teleological entity. A deity would imply that this supernatural being has contact with the human race and that would not necessarily be true. But without a final cause, you have the problem of infinite regression. So, are you referring to deity in the above quote in the context of a supernatural being that has contact with humans? Not meaning a supernatural, final cause?

I don't think that ID necessarily leads back to some type of supernatural entity, as I attempted to explain to Tangle.

Here's why:

1. That certain biological features on earth could not have plausibly evolved says nothing of whether an intelligence existing elsewhere in the universe could evolve. In the first place, there are a whole bunch of possible forms of intelligence that could, in theory, evolve. And once you grant that this is possible then there is no basis for arguing that ID must invoke a supernatural being at some point.

2. The argument that ID leads back to a supernatural being only works if the ID position is that biological feature X could not have plausibly evolved. Although this is admittedly the position of the vast majority of ID proponents, if the ID position is that biological feature X could have evolved but was in fact intelligently designed, ID does not necessarily trace back to a supernatural entity.

3. Finally, in response to the question "Who or what designed the designer," there is a very simple, but reasonable, answer: I don't know.


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Genomicus
Member (Idle past 1215 days)
Posts: 852
Joined: 02-15-2012


Message 156 of 167 (672046)
09-02-2012 12:40 PM
Reply to: Message 129 by herebedragons
08-21-2012 10:46 PM


Without purpose don't we just have evolution?

Quite right, but if we find evidence of intelligent design (through front-loading), wouldn't that, by definition, imply purpose?


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Genomicus
Member (Idle past 1215 days)
Posts: 852
Joined: 02-15-2012


Message 158 of 167 (672051)
09-02-2012 3:02 PM
Reply to: Message 157 by Percy
09-02-2012 1:40 PM


If you're right that you avoid the requirement for a supernatural designer by not claiming that certain biological features couldn't evolve naturally, then without that claim and in the absence of any evidence what drives your belief in front-loading?

The key phrase here is "in the absence of any evidence." The problem though is that I think that there are some clues in favor of front-loading.

If you claim unlikelihood of natural evolution (as opposed to impossibility) then that's just the Dembski position, which is part of the ID mainstream you supposedly eschew.

I do question the efficacy of Darwinian evolution to produce certain biological features, but that's not my main focus. Nevertheless, the presence of a discontinuity in the biological universe is one hallmark of intelligent design, and thus a suspicion in favor of ID.

Edited by Genomicus, : No reason given.


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 Message 159 by Percy, posted 09-02-2012 4:14 PM Genomicus has taken no action

  
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