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Author Topic:   Does ID predict genetic similarity?
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Message 4 of 167 (670065)
08-08-2012 10:53 AM
Reply to: Message 1 by herebedragons
08-07-2012 10:21 PM

I was having a discussion with someone about using genetic similarity as evidence for relatedness and this issue came up. It was suggested that genetic similarity is also compatible with ID as well as common descent so it is ambiguous as to relatedness. I agreed that it is indeed compatible with both ideas. However, I suggested that common descent predicted similarity while ID did not.

Talkorigins has a well written paragraph on this topic which echoes my own thoughts:

The nested hierarchical organization of species contrasts sharply with other possible biological patterns, such as the continuum of "the great chain of being" and the continuums predicted by Lamarck's theory of organic progression (Darwin 1872, pp. 552-553; Futuyma 1998, pp. 88-92). Mere similarity between organisms is not enough to support macroevolution; the nested classification pattern produced by a branching evolutionary process, such as common descent, is much more specific than simple similarity. Real world examples that cannot be objectively classified in nested hierarchies are the elementary particles (which are described by quantum chromodynamics), the elements (whose organization is described by quantum mechanics and illustrated by the periodic table), the planets in our Solar System, books in a library, or specially designed objects like buildings, furniture, cars, etc.

It goes further than similarity. It is the PATTERN of similarity that matters. That pattern is a nested hierarchy. There is simply no reason that an intelligent designer would separately create species so that they fall into a nested hierarchy. Even humans do not obey this pattern of similarity when we design organisms. For example, we have no problem taking the GFP gene from jellyfish and putting it in bony fish to produce Glofish. Our own designs for cars and furniture do not fall into a nested hierarchy even though these designs borrow from other designs.

So why would a designer limit itself in order to produce a pattern of similarity that evolution would produce?

The problem grows for ID supporters if we assume an omnipotent designer. ID supporters will often claim that it "makes sense" to copy other designs. But does that hold true for an omniscient, omnipotent designer who has unlimited resources? NO. A designer with these attributes would expend as much energy starting from scratch as it would copying previous designs. Reusing designs only makes sense for designers like us who are limited in ability, knowledge, time, and resources.

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Message 9 of 167 (670088)
08-08-2012 4:35 PM
Reply to: Message 5 by herebedragons
08-08-2012 2:01 PM

Anyway the designer wants to do it is acceptable, so how would you determine if it was not due to a designer?

One important factor to point out is that any potential observation can be explained by ID, therefore none are. The fact remains that evolution predicts a specific pattern, and we observe that pattern. That is one leg up for evolution.

After I made this point I was accused of automatically rejecting any possibility of a designer. I feel my position did not exclude the possibility of a designer, but it says that genetic similarities or nested hierarchies do not predict a designer. Your position does seem to go further and reject the possibility of a designer.

I am merely pointing to the absurdity of a designer limiting itself to a nested hierarchy just to make life look like it evolved when in fact it didn't. I see no logical reason why a designer would do that, other than to be a deceiver.

We could extend this same logic to other theories. For example, we could say that there is some magical force that causes diseases and that the correlation between microorganisms and disease is just happenstance. It makes no sense.

The reasonable conclusion is that we see a pattern of shared features that matches the predictions made by the theory of evolution because species evolved.

On the other hand, nested hierarchies are not unknown from nature outside of biological systems. The universe is ordered as such:
planet --> solar system --> interstellar neighborhood --> galaxy --> supercluster --> observed universe

also in ecology
biotype --> ecosystem --> ecoregion --> biome --> ecozone --> biosphere

Those are not based on shared and derived physical characteristics. Rather, they are based on scale.

But I still don't see that ID predicts that organisms be organized in a nested hierarchy but it also doesn't exclude the possibility of a designer.

It is impossible to exclude magic. The world could be 2 minutes old with an embedded history and embedded memories and we would never know it. However, there is no compelling reason to believe that a 2 minute universe is true. In the same way, there is no compelling reason to think that a designer created life on Earth. However, there are compelling reasons to think that evolution did occur. That is the difference.

Edited by Taq, : No reason given.

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Message 19 of 167 (670370)
08-13-2012 1:11 PM
Reply to: Message 13 by herebedragons
08-12-2012 10:46 PM

But does common descent actually predict aspects like parallel evolution or convergent evolution or is this an explanation of an observation? If a common ancestor was designed or "pre-programmed" with certain genetic traits it would be predictable that the trait would arise in separate lineages.

We observe that different species have different adaptations for the same function. For example, the design of the bird and bat wing are very different, but they serve the same function. The explanation for this observation is convergent evolution where the same selective pressures acted on different ancestors to produce different solutions to the same problem.

As to the second part of the quote, we don't see the same trait evolving independently in different lineages. What we see are htings like the bird and bat wing. These are superficially similar adaptations, but they differ drastically in the details.

I would also suggest that [cosmological bodies] are indeed organized based on shared characteristics as well as scale.

I would be very interested in seeing how this works. For example, do we put the Sun and the gas giant planets in the same group because they share the characteristic of being made out of gas? Do we put the moons of Jupiter and the Earth in the same category because they are made of rock? It would seem to me that there is no way of producing single ranked system based on shared characteristics. However, we can do that with life. As talkorigins puts it:

Although it is trivial to classify anything subjectively in a hierarchical manner, only certain things can be classified objectively in a consistent, unique nested hierarchy. The difference drawn here between "subjective" and "objective" is crucial and requires some elaboration, and it is best illustrated by example. Different models of cars certainly could be classified hierarchically—perhaps one could classify cars first by color, then within each color by number of wheels, then within each wheel number by manufacturer, etc. However, another individual may classify the same cars first by manufacturer, then by size, then by year, then by color, etc. The particular classification scheme chosen for the cars is subjective. In contrast, human languages, which have common ancestors and are derived by descent with modification, generally can be classified in objective nested hierarchies (Pei 1949; Ringe 1999). Nobody would reasonably argue that Spanish should be categorized with German instead of with Portugese.

The difference between classifying cars and classifying languages lies in the fact that, with cars, certain characters (for example, color or manufacturer) must be considered more important than other characters in order for the classification to work. Which types of car characters are more important depends upon the personal preference of the individual who is performing the classification. In other words, certain types of characters must be weighted subjectively in order to classify cars in nested hierarchies; cars do not fall into natural, unique, objective nested hierarchies.

Because of these facts, a cladistic analysis of cars will not produce a unique, consistent, well-supported tree that displays nested hierarchies. A cladistic analysis of cars (or, alternatively, a cladistic analysis of imaginary organisms with randomly assigned characters) will of course result in a phylogeny, but there will be a very large number of other phylogenies, many of them with very different topologies, that are as well-supported by the same data. In contrast, a cladistic analysis of organisms or languages will generally result in a well-supported nested hierarchy, without arbitrarily weighting certain characters (Ringe 1999). Cladistic analysis of a true genealogical process produces one or relatively few phylogenetic trees that are much more well-supported by the data than the other possible trees.

From my point of view, cosmological bodies would suffer the same problem as cars when it comes to organizing based on shared characteristics.

Magic implies human attempts to influence events by spells, incantations, etc. And while I am sure there are some that treat the supernatural as magic, there is a distinction. If you merely mean that supernatural events are outside of scientific understanding or detection, then I totally agree.

Magic implies the supernatural. That is what it has always implied. It is MEANT to be kept outside of any attempt to test or verify. Calling something "supernatural" is just another way of saying "don't question it".

Sure there are compelling reasons to believe that evolution occurred, but I don't think that evolution answers all questions about our existence. Perhaps you do, but I sure don't. That doesn't mean that I think we need to appeal to the supernatural to explain something in the natural world we don't understand, but how can we dismiss the possibility outright?

Why should we consider it in the first place? Simply because it could be true? If so, then why not hold a belief in a 2 minute universe that can not possibly be supported by anything other than dogmatic belief alongside the evidenced based conclusion of a 13+ billion year old universe?

Why not start from a position with no beliefs, and then follow the evidence?

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Message 31 of 167 (670423)
08-14-2012 12:53 PM
Reply to: Message 28 by herebedragons
08-14-2012 10:26 AM

So you agree that the ToE does not predict convergent evolution, but merely explains the phenomenon?

Since evolution is a blind stochastic process we can't predict any specific outcome. We could use the double slit experiment as an analogy. In this experiment a photon will pass through two slits at once and interfere with itself. This produces an interference pattern on the other side of the slits. However, it is impossible to predict where any single photon will land. All you can do is predict the overall structure of the interference patterns. Evolution is the same. You can't predict the path of a single lineage, but you can predict that the overall pattern of shared and derived characteristics will fall into a nested hierarchy.

Perhaps I should have said that the same trait evolves independently in separate taxa. Homoplasy is common and can make classification difficult as sharing a trait does not mean the organisms are directly related. My point is not that this disproves evolution or automatically make phylogenies wrong, it is simple that the ToE does not actually predict homoplasy, rather it allows them and explains them. Do you agree or disagree? If you disagree, how does the ToE predict homoplasy?

I would agree that homoplasies can occur. The ToE does not predict that they have to happen, but the mechanisms of evolution are certainly capable of producing them. It's a bit like asking how the laws of gravity and erosion could predict the Grand Canyon. Of course, they can't, but the mechanisms are certainly capable of producing the Grand Canyon.

However, there is no way for DNA sequence to hop from one branch to another, at least for metazoans. The ultimate check is DNA. At the same time, you can have incomplete sorting of traits which can muddy the waters, but that is somewhat predictable.

When I was a kid I dug a hole in our backyard. It was about 4 foot deep so that I could almost completely stand up in it. I was convinced that just a few more feet and I would be through the Earth and into China. (But my mom found out about it and made me fill it in before I could complete the task). This is how I view searching for the supernatural with science; we say we have dug down 4 feet (maybe a better equivalent of our modern knowledge would be a mile deep) and we haven't found the supernatural yet, so there must not be any. And others say that with just a few more feet of digging we will find it. But, as much as we know about the universe, I don't think we have even scratched the surface.

So as far as science goes, I agree that science is the search for natural causes, not the search for supernatural causes. But philosophy is the search for answers to questions that science cannot answer. Science is NOT the end-all argument.

To use your analogy, we have been digging for thousands of years and found nothing. We have been using science for just a few hundred years and it has been spectacularly successful. This is why science is held in such higher regard. Science WORKS. It produces knowledge where supernatural explanations failed after thousands of years of trying. As Steven Weinberg put it:

"Once nature seemed inexplicable without a nymph in every brook and a dryad in every tree. Even as late as the nineteenth century the design of plants and animals was regarded as visible evidence of a creator. There are still countless things in nature that we cannot explain, but we think we know the principles
that govern the way they work. Today for real mystery one has to look to cosmology and elementary particle physics. For those who see no conflict between science and religion, the retreat of religion from the ground occupied by science is nearly complete"
(Weinberg, S., "Dreams of a Final Theory," Pantheon: New
York NY, 1992, pp.249-250)

The supernatural was once held to be the answer for everything. Now it doesn't explain anything. The supernatural is irrelevant and superfluous to our understanding of how reality works. Not once have we found a verifiable supernatural mechanism while we have found millions of natural mechanisms.

The real question is why should we even consider supernatural explanations?

No one ever comes from a position of NO beliefs. Beliefs are foundational to our personalities, our attitudes, our behaviors. Everyone is indoctrinated with beliefs of one type or another at a very early age (some research suggest that our basic personalities and basic belief systems are formed by age 5). Some people cling to their beliefs more tightly than others. Some are willing to adjust or abandon their beliefs based on physical evidence.

What I am saying is that we should try to put those beliefs to the side as best we can, and then follow the evidence. Or better yet, start by justifying those beliefs based on evidence, reason, and logic.

But all this is really off topic. I don't need to justify the question "Does ID make predictions that the ToE does not?" That question does not even start with the assumption that there is an intelligent designer. It is asking a question about the "theory" of ID. Whether there are supernatural explanations or not is irrelevant. If ID is to be considered a legitimate science it needs to make predictions about physical evidence that we can discover and those predictions need to be contrary to what we expect to find with the ToE.

I hope that my posts have helped to answer that question.

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Posts: 8488
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Message 42 of 167 (670481)
08-15-2012 4:52 PM
Reply to: Message 40 by Genomicus
08-15-2012 4:09 PM

You did not address my argument at all in the above. My argument is that if one argues that bad design is evidence against ID, then rational design is evidence in favor of ID.

Given that life falls into a nested hierarchy, it can be argued that the whole of life is not rationally designed. No designer would limit themselves to a nested hierarchy. None. There is no rational reason to do so. Us humans don't even force our designed organisms into a nested hierarchy. Instead, we freely move genes from species to species without any care about a nested hierarchy.

Let me put it this way: why exactly is poor design of a biological system an argument against the engineering of that system?

It is an argument against a competent designer (i.e. God). It could be argued that poor designs are evidence of a poor designer, but given the theological views underpinning ID these arguments are rarely used.

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Message 62 of 167 (670585)
08-16-2012 12:04 PM
Reply to: Message 59 by herebedragons
08-16-2012 9:02 AM

But isn't that assuming that the nested hierarchy we observe today was the same product the designer originally produced? Very few people still hold to the fixity of species (although there are still some ). Even in the most extreme case, if everything was created only 6000 yrs ago and rapidly diversified after the flood we would still expect a nested hierarchy of sorts, just with large discontinuities between "kinds". The further back you push the "creation event" the smaller those discontinuities would appear. Until, on the other extreme, you have a situation like genomicus proposes that the designer "front-loaded" the LCUA and then we would expect the exact nested hierarchy we observe today.

In order for ID to work in this paradigm you would have to push the designing back to a single ancestor of all life in the very distant past. As you say, there will be discontinuities between created kinds. There is no reason why created kinds should fall into a nested hierarchy. If ID is the argument that the designer plopped a simple RNA replicator on Earth and all life evolved from there then I really don't see any clash between Evolution and ID.

But I don't think the fact that life can be organized into a nested hierarchy excludes the existence or involvement of a designer.

Nothing can exclude the supernatural because the supernatural is unfalsifiable.

Again, this is assuming that what we observe today is the same product that was initially designed.

Let's use the recurrent laryngeal nerve (RLN) as our example. In tetrapods this nerve exits the spinal column, goes down through the neck into the chest, loops under the aorta, goes back up the neck, and then connects to the larynx very close to the spot where the nerve exits the spinal column. This is analogous to running an extension cord across your living room, looping it around the couch, and then back to the tv even though the plug in is right by the tv. It is just poor design.

So how do we solve this problem? Since this is common to all tetrapods does this mean that the common ancestor of all tetrapods did not have this poor design to start, but later developed this trait? Or did all tetrapods at a much later date (after the flood?) independently evolve this clumsy design? What about the inverted retina in all vertebrates? Do we now have to go back to a designed common ancestor of all vertebrates, or independent evolution of an inverted retina across all vertebrate created kinds? Both seem very problematic from an ID perspective.

I think the issue of "poor design" says more about the nature of the material world than it does about the nature of the designer. If this world were designed to be perfect in every way, wouldn't it be more of a supernatural world? But instead, the material world is subject to degradation, decay and death. Could a designer have designed a perfect world? I suppose so, but instead he made it a material universe rather than supernatural.

From everything I have seen, it appears to be a material world operating all on its own without any supernatural influence. That would seem to be the simplest explanation. A deist type position is about the best you could do, IMHO.

I saw someone arguing that he didn't believe in a designer because he had gotten a cavity. He mused that a good designer would have given us titanium teeth that never decay. Really? That's the criteria for a good designer? its not a DNA molecule that can replicate and repair itself, be passed on to the next generation, mutate to allow for diversity, package itself so as to fit within a single cell, etc... I have pretty bad teeth myself, maybe its because I drink too much pop and eat too much candy...

That same mutating DNA molecule also produces disease. Would an omnipotent and omniscient designer leave us with biological systems that produce children with devastating and painful cancers? It would seem to me that such a designer would have to purposefully include this in the design. This is not something that would just slip by quality assurance. Such a designer would have to consciously decide that yes, children will die an early and painful death because of this design.

But I think you hit on a major problem with the ID movement when you said "theological views underpinning ID". Rather than asking where does the philosophical ideals and the scientific ideals overlap they try to turn their philosophical ideals into scientific processes. And so far have failed to have those ideals accepted in the scientific realm.

I would suggest that their philosophical ideals force them to ignore the evidence, and then propose ideas that are not supported by the evidence.

Edited by Taq, : No reason given.

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Message 64 of 167 (670606)
08-16-2012 1:22 PM
Reply to: Message 63 by Genomicus
08-16-2012 12:57 PM

The story goes on, of course, but the point is this: certainly, even if our own biological life could not have plausibly evolved, it is possible that other forms of intelligence exist which could evolve.

If we are going to keep the origin of this intelligence within our universe, then we have a rather interesting problem. Our universe has a finite history. That designer had to evolve naturally without the help of another designer at some point in our universe's history. I think there is every reason to believe that we are that designer.

Also, the question is a bit irrelevant to me because, for the most part, I'm trying not to argue for ID based on the implausibility of evolution but rather based on positive evidence for ID. In other words, it is perhaps possible for non-teleological processes to produce life but this does not mean that these processes did produce life. When discussing biological origins, it must be remembered that we are talking about actual history and not about what could have been.

The problem posed by the opening post is more subtle than this. I think even ID proponents agree that if common ancestry is true then we should see shared DNA between species. No one is arguing that shared DNA is an implausible outcome of evolution.

What ID proponents seem to be doing (not necessarily you, but other ID proponents as discussed in the opening post) is trying to have ID produce the same evidence that evolution would. This is an attempt to save the ID hypothesis. It certainly violates Occam's Razor, but that is just a rule of thumb so it can worked around. However, this position is very hard to rationalize. What it boils down to is a designer going out of its way to make life look like it evolved (at least for ID models where complex life is separately designed).

We humans certainly do not do this. For example, we stuck an exact copy of the GFP gene into vertebrate fish allowing them to glow under UV light. We didn't go out of our way to change the sequence of the GFP gene so it would appear to be distantly related to jellyfish, and then stick the same GFP gene in all of the species necessary to make it look like the GFP gene was present in the common ancestor of vertebrates and cnidarians. Why would we? If we wouldn't, why would another designer do that? It makes no sense at all. It runs counter to what we would consider intelligence.

In summary, the argument that ID necessarily leads back to a deity is not at all rigorous and makes several problematic assumptions.

That depends on the ID model. I think we are all well aware of ID proponents who argue that an intelligence like ours can not be produced naturally.

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Message 80 of 167 (670656)
08-16-2012 8:27 PM
Reply to: Message 77 by Genomicus
08-16-2012 8:05 PM

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

Since the mechanisms of evolution are driven by relative fitness, not optimal design, I don't see why it would need to.

Of course, there can be a relationship between optimal design and fitness, but one is not dependent on the other. Evolution is BLIND to design. It doesn't "see" how a design is put together. If a change produces an increase in fitness then that change is kept, even if that change leads to bad design (e.g. the inverted vertebrate retina).

Also, evolution can't start from scratch. Evolution works with what is already there. From a design perspective, you would not start with a fish and then try to design a tetrapod from that fish. However, that is where evolution had to start from. Due to this we get really bad design choices, such as the recurrent laryngeal nerve that takes a wild route through the body due to changes in gill structures.

However, a designer can start fresh. A designer can consider the problem and start with a set of subsystems that make sense. A designer does not have to start with a fish, and then make a tetrapod from that fish. A designer can start with a forward facing retina and not be stuck with an inverted retina just because other vertebrates happen to have one.

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.

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Message 82 of 167 (670658)
08-16-2012 9:00 PM
Reply to: Message 81 by Genomicus
08-16-2012 8:46 PM

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.

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

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.

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.

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.

I strongly disagree. Even Behe admits that biological systems can best be 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:

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.

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

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Message 91 of 167 (670692)
08-17-2012 10:42 AM
Reply to: Message 84 by Genomicus
08-16-2012 11:20 PM

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.

A nested hierarchy incorporates both homologous and derived features.

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."

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.

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.

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.

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).

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

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.

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

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

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.

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Message 97 of 167 (670723)
08-17-2012 3:32 PM
Reply to: Message 92 by Genomicus
08-17-2012 11:10 AM

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.

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.

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?

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

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.

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.

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."

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)."

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.

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.

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

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.

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.

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

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

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.

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.

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Member (Idle past 31 days)
Posts: 8488
Joined: 03-06-2009

Message 106 of 167 (670854)
08-20-2012 10:26 AM
Reply to: Message 104 by herebedragons
08-20-2012 9:07 AM

But do you think that a perfect world without death and suffering is the prediction of an ID hypothesis?

I think this speaks more towards the theological implications. It is more of a question aimed at one type of a designer (e.g. an omnipotent caring god).

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.

It only goes to the larnynx and around the larynx as far as I know. There are connections to the esophagus and trachea, but again this is a circuitous route for these features.

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.

Not really sure, but I would strongly suspect that the development of the nerves and neck vertbrae are strongly linked. The RLN still makes that same trip in giraffes as well resulting in 15 feet (IIRC) of extra nerve fibers just to make this strange route.

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.

I appreciate the effort, but at the end of the day we arrive at the same problem, a lack of a solid method for differentiating between ID and evolution. Genomicus has proposed front-loaded evolution which makes predictions post hoc. It boils down to a sharpshooter fallacy. Which genes were front loaded? Well, the ones that became ubiquitous. That is drawing the bull's eye around the bullet hole. Whatever evolves it will be claimed that it was front loaded.

Edited by Taq, : No reason given.

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Member (Idle past 31 days)
Posts: 8488
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Message 140 of 167 (671142)
08-22-2012 3:13 PM
Reply to: Message 137 by herebedragons
08-22-2012 11:10 AM

Re: universal principles
The discussion of origins is not just an issue of science, but about the history of our existence. In the pursuit to understand the origin of life and indeed the universe, our search should be for truth. IF there was a designer science should seek to know that. Science doesn't NEED there to be a designer to continue to be science, but in order for science to be the "truth" then it needs to find the answers that are true. So, IF there is a designer, then science NEEDS it.

What science should do is follow the evidence. By saying "IF there is a designer . . ." you are jumping the gun. If the evidence leads to a designer then it will lead there. There is no need to project our hopes in the existence of a designer onto the science.

Ockham's is not a scientific law that can be tested against, but rather a principal or a guideline that helps scientists develop theories. A simple explanation is not always the best or the correct one (I may be even willing to say that a simple explanation is rarely the best or correct choice, but I don't want to have to support so bold a claim). Ockham's is not a test we apply to judge failure or success, we need to chose the hypothesis that is most correct or has the best explanatory power.

Occam's Razor is a way of detecting exactly what I describe above, projecting our hopes onto the science when there is no evidence for those hopes. As to the topic in this thread, we find that the evidence is consistent with evolutionary mechanisms. Some would argue that perhaps ID is still true and that ID just produces evidence that is indistinguishable from the process of evolution. This is a case of projecting hopes onto the science. There is no reason why that explanation is needed. It multiplies unnecessary assumptions.

Evolution is the best explanation because evolution is evidenced and capable of producing what we observe. The best explanation is the one that passes Occam's Razor.

That said, I don't think science has the ability or the tools (and maybe never will) to address the issue of a designer and the issue of origins in general. In the sense that science is intended to understand the natural world, a supernatural explanation is superfluous. But that doesn't mean we should stop our pursuit for the truth.

Science does have the ability to test mechanisms that produce empirically verifiable observations. Therefore, ID is testable whether you want to claim that it is due to the supernatural or not. People claiming that Thor produces lightning did not stop science from studying and then explaining lightning. The label "supernatural" is nothing more than a warning that people don't want you to question their explanation.

Science does have the tools to explain our origin and the origin of the universe. The only problem is that some people are afraid that the answer will differ from the one they want.

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 Message 137 by herebedragons, posted 08-22-2012 11:10 AM herebedragons has responded

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Member (Idle past 31 days)
Posts: 8488
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Message 150 of 167 (671328)
08-24-2012 11:39 AM
Reply to: Message 145 by herebedragons
08-24-2012 9:46 AM

Re: universal principles
My issue is with something different. My problem is with the philosophical worldview of naturalism, the belief that nature is all there is, and was and ever will be. Everyone brings a worldview (a system of beliefs) to this debate about origins. It is a starting point for your understanding of the universe. You may be able to modify and adjust your worldview, but no one comes to this debate neutral.

I really don't see this as a hurdle for ID or for assessing the supernatural and its effects on the natural world. For all intents and purposes, we can drop naturalism from science. What science uses is empiricism. If the supernatural has effects on the natural world then we can detect it through empiricism. There is nothing in the scientific method that precludes the supernatural.

It would appear that ID supporters have a vested interest in keeping science away from the supernatural. Once you bring in science then beliefs are suddenly put to the test. They can't have that. In so many ways, the supernatural is nothing more than a set of dogmatic beliefs. It is a collection of claims that no one wants challenged.

So, let me propose a hypothesis based upon my worldview.

"Everything in this universe ultimately owes its existence to a divine creator."

What evidence led you to form this hypothesis?

But does my theory have more explanatory power than the current theory? Well, it includes or allows all of the current theory, so it is equal in that regard. In addition, it has the power to explain the origin of the singularity and what existed before the singularity. It can explain why the universe is so extremely ordered and why there are principals that govern its day-to-day operation. It explains the fine tuning that we observe in natural phenomenon.

So what experiments do we construct to test this hypothesis? How do we determine if it is true?

Now, in order for me to gain support for my hypothesis and have it accepted as a scientific theory, I need to make valid predictions and support those predictions with evidence.

Uhmmm ???? ahhh??? let's see .... a little help here ....

This is the point of this thread! Not whether it is a valid question to ask in the first place. If you approach this with the view that "nature is all there is, and was and ever will be," then of course you will see it as an invalid hypothesis. I believe GDR said that the premise of this tread assumed the existence of a designer. Well, that is not exactly correct. It assumes a worldview that nature is NOT all there is!

The point is that good explanations produce testable predictions. Beliefs in the supernatural as described by ID supporters do not produce testable predictions. They are not good explanations. They are very poor explanations. Frankly, we are better off with "I don't know" as an explanation than "some supernatural deity did it somehow in some way that no one will ever describe".

History bears this out as well. To paraphrase Steven Weinberg, at one time nature could not be explained without nymphs, dryads, and fairies. With the advent of science we quickly learned that the supernatural was not controlling the world around us. Instead, there were mindless mechanisms ticking away that were not magical. We found out that lightning is not produced by Thor, fermentation is not produced by Bacchus, and no god is producing clouds. Now we are told that there is still supernatural magic going on, and once again it exists where we are most ignorant of reality. Namely, gods can now be found at the singularity that birthed our universe. Gods are always just beyond the horizon of our knowledge, at least that is what we are told, and yet every time we crest that next ridge obscuring our vision we don't find any gods. We keep finding mindless mehcanisms ticking away that really don't care about us or anything for that matter. So why should we expect to find gods in that singularity when that explanation has failed so spectacularly in the past?

No it does not. Science can only go so far. It has limits.

Yes, science is limited by what is real. Science can not support theories that are not true or made up. I don't see that as a problem, but I can see why some ID supporters would have a problem with it. We use science because it does have limits. It is the limits that make it useful. If not for those limits then every explanation would be true, no matter what that statement was. We would be awash in solipsisms and post-modernism, none of which are useful.

If we throw those limits out then how can we ever determine if something is true or false?

Excluding the divine from the discussion excludes a whole realm of possible explanations while providing no additional information.

That is not what is happening. We are not including fantasies and unevidenced claims. Why should we? It is not the fault of science that theists are unable to evidence their claims. That is a failure of theism, not science.

I agree. But it goes both ways.

Given the lack of research amongst ID supporters I would say that it doesn't go both ways.

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