Which is falsifiable?

[sandy_mcd]

Neo-darwinists including BeGood like to use the term 'self-assembly' to account for anything that occurs within the cell even if the pieces being assembled are being assembled not by just falling into place based on chemical affinities but because they are literally being picked up and carried by other parts of the cell. To truly seperate what is true 'self-assembly' from what is conjecture, ask yourself if you could get the same result without the rest of the cell. In other words, if I took the proteins that together form a flagellum and dumped them into a petri-dish, would I end up with a pile of proteins or a flagellum? This has been tried countless times including by Dr. Behe. You get a pile of proteins. No self-assembly occurs.

I think we all agree that
1) If you take a bunch of amino acids (in the same proportions as found in some protein), put them in a jar, and shake them up, you will not get the protein.
2) If you took a protein synthesizer which could link amino acids and dumped the same mixture of amino acids into it, you would not get the protein.
3) DNA, RNA, and a host of other requirements are necessary for proteins to be formed from amino acids in cells.

[If people are already using a word or phrase, such as self-assembly, to mean something, it ill behooves others to use the word or phrase with a different meaning, even if they disagree with the conventional meaning.]

[sandy_mcd]

Darwinists have no answer for how the flagellum developed but they say linking it to intelligence is an argument from ignorance and unfalsifiable.

A reference a few posts ago was to a protein which could be denatured in the presence of urea. Urea is a simple organic molecule found in the urine. The synthesis of urea was first reported by Wohler in 1828.
According to Cohen and Cohen, J Chem Ed Vol 73 #9 1996 pp 883-886:
" The significance of this work lies not just in the first synthesis of urea but also in its effect on the then-popular belief - called "Vitalism" - that such a preparation was impossible, because all syntheses of organic materials required the presence of a "Vital Force". This force or power was neither understood nor even uniformly explained; nevertheless, it provided the distinction between living and dead materials. To a modern chemist, the validity of Vitalism might be redefined as how to artificially form a carbon-carbon bond, but for scientists of a century-and-a-half ago, bond formation, let alone the existence of atoms, was a hazy idea at best."
Of course, as some might guess, many held onto a belief in Vitalism for some time afterwards.

[Wall-dog]

This is a pretty reasonable refutation of your statements above. An isolated protein is active in solution. As the concentration of urea increases, the protein loses some of its three-dimensional structure and no longer functions. As the urea is removed, the structure and function return. [Again, you are confusing molecular conformation and crystal packing.] There is no DNA present. There is no RNA present. The protein regains its complex three-dimensional structure on its own, just as virus subunits will spontaneously form viruses.

Sandy,

That is a good illustration, but it doesn't refute anything I've posted. Nobody questions the fact that proteins, once assembled, fold. In fact I've posted that myself. I've never seen that you could get them to unfold by increasing the urea in a solution within which they are contained but really since they fold themselves it isn't surprising that they could be caused to unfold given the right chemical combinations. But they still have to be assembled first.

I think we all agree that
1) If you take a bunch of amino acids (in the same proportions as found in [some protein), put them in a jar, and shake them up, you will not get the protein.
2) If you took a protein synthesizer which could link amino acids and dumped the same mixture of amino acids into it, you would not get the protein.
3) DNA, RNA, and a host of other requirements are necessary for proteins to be formed from amino acids in cells.

I would hope we would agree to that! Thank you for putting it succinctly.

"Usually, even a non-Christian knows something about the earth, the heavens, and the other elements of this world, about the motion and orbit of the stars and even their size and relative positions, about the predictable eclipses of the sun and moon, the cycles of the years and the seasons, about the kinds of animals, shrubs, stones, and so forth, and this knowledge he holds to as being certain from reason and experience. Now, it is a disgraceful and dangerous thing for an infidel to hear a Christian, presumably giving the meaning of Holy Scripture, talking non-sense on these topics; and we should take all means to prevent such an embarrassing situation, in which people show up vast ignorance in a Christian and laugh it to scorn. The shame is not so much that an ignorant individual is derided, but that people outside the household of the faith think our sacred writers held such opinions, and, to the great loss of those for whose salvation we toil, the writers of our Scripture are criticized and rejected as unlearned men. If they find a Christian mistaken in a field which they themselves know well and hear him maintaining his foolish opinions about our books, how are they going to believe those books in matters concerning the resurrection of the dead, the hope of eternal life, and the kingdom of heaven, when they think their pages are full of falsehoods on facts which they themselves have learnt from experience and the light of reason? Reckless and incompetent expounders of holy Scripture bring untold trouble and sorrow on their wiser brethren when they are caught in one of their mischievous false opinions and are taken to task by those who are not bound by the authority of our sacred books. For then, to defend their utterly foolish and obviously untrue statements, they will try to call upon Holy Scripture for proof and even recite from memory many passages which they think support their position, although “they understand neither what they say nor the things about which they make assertion.”

Are you asserting that I'm talking nonsense and am thus a dangerous false prophet? One of the reasons I am very careful to make sure that I can back my claims with expert testimony is because I don't want to fall into that pit. That is also why I post the conclusions and link to the evidence instead of posting the evidence and making my own conclusions. I don't want to make assertions that are not fully supportable so I don't make any at all. I use the assertions made by others who have far more experience and knowledge on these topics than I do. A wise man knows his limitations.

But you have fact, and then you have what can be inferred from fact. Most debate centers around inference rather than fact. The neo-Darwinist infers that some form of self-assembly must exist because, as BeGood put it, what else could explain it? The ID proponent calls for a known force - intelligence.

[BGoodForGoodSake]

Walldog lets start with the process.

A protein is formed through several steps.
First the DNA is unzipped at a start codon. And is transcribed until it reaches a stop codon. This is Transcription. We will refer to this as step 1 in our conversations.

DNA is composed of a nitrogenous base and a sugar phosphate backbone.
http://www.geneticengineering.org/chemi ... id/DNA.htm

This structure is important, because the phosphate bonds do not have an affinity, meaning AG is just as likely as AC or CC or and number of combinations. The nitrogenous end however always is complementary. A with T and C with G.

This is how duplication is possible. Because the affinity for its complement allows the individual nucleic acids to form a chain in the correct sequence in the complementary chain.

Now the next step is Translation. The mRNA finds its way to a ribosome. Here tRNA bonds with the mRNA and releases corresponding aminoacids. So how is the information in the DNA translated to aminoacid chains?

Each tRNA has an affinity with a specific amino acid. Also on the other side tRNA has an affinity to its complement. tRNA in the ribosome will liberate the attached aminoacid which will form bonds with the previous and next amino acid in the chain. Lets call this step 2 from here on out.

Next the protein folds. This is step 3 and I think you would agree here that proteins fold according to their amino acid sequence.

And finally we have step 4. The proteins begin interacting with each other. Here the interactions are also due to chemical reactions. And charge interactions. This is the quaternary structure of the protein. But protein interactions can go beyond this as well.

As you can see the DNA encodes the specific sequence of amino acids, and due to natural forces the resulting protein forms. Any change to the DNA will result in a different protein. The change will carry through step 1 2 and 3 and effect the final form of the protein. And effect step 4 as well because form defines property.

How and if it effects the function of the protein depends on where the change occurred.

That takes us to step 5. Mutation. Mutations do occur. Whether a series of mutations does or doesn't account for the origin of the flagellum is up for debate. However it is clear that mutations will result in new proteins.

Hers another account.
Please read this Walldog.
http://web.jjay.cuny.edu/~acarpi/NSC/12-dna.htm

[Wall-dog]

BeGood,

Nowhere in your sources does it say anything about proteins assemblying themselves. It talks about the assembly occurring within the cell but it shows the rest of the cell as being an integral part of that process.

Just out of curiosity, do you read your sources before you post links to them? Perhaps you should. In fact, I would ask that you quote the relevant parts because sometimes they are difficult or impossible to find. When you write something and then just provide a link to a really long article or a slide show or something, you are making it very difficult to determine what parts of what you have written are supported by the source and what parts are conjecture on your part. I would ask, again, that you quote the relevant parts so that we don't have to go searching for them. The benefit of the link is that it allows us to quickly check the context of the quote. When all you give is the link you make it much harder to verify the source and particularly so when often you have more conjecture in what you have written than your sources justify.

I think I understand now where you are confused though. You seem to think ID embodys intelligence into the cell - like Dr. Behe and Dr. Meyer think the proteins themselves are intelligent beings and are using intelligence to assemble themselves. That is not the case. Dr. Meyer, Dr. Behe, and other ID proponents don't argue that the cell is intelligent. Rather they argue that intelligence was a part of the process in creating the cell. They point to the cell's ability to create flagella as proof of that intelligence. Nobody is suggesting that the cell itself has intelligence. Of COURSE there are mechanisms within the cell that allow it to create proteins and assemble them into the various components that it needs. Affinities within the cell are a big part of that.

Also, we aren't just talking about creating flagella. We are talking about creating the flagellum. How did it initially come to be? How do you create a flagellum without the mechanism for creating it already in place? How does it come from other, less complex components? You can't just quote sources that take the existance of flagella for granted and show us how a system designed to create flagella works. That doesn't meet the challange. You need to show how the first flagella was created. If all I wanted from you was a biology lesson it wouldn't have been a very good challange.

But the process of building a Flagellum is much more involved than you are letting on. Even though the process doesn't really explain how the first flagellum came about, why don't we illustrate it just to show how complex it really is.

To quote Dr. Behe from Strobel's The Case for a Creator:

"The cell is not a simple bag of soup, with everything sloshing around. Instead, eukaryotic cells - cells of all organisms except bacteria - have a number of compartments, sort of like rooms in a house.

There is a nucleus, where the DNA resides; the mitochondria, which produce energy; the endoplasmic reticulum, which processes proteins; the Golgi apparatus, which is a way station for proteins that are being transported elsewhere; the lysome, which is a garbage disposal unit; and the perixisome, which helps metabolize fats. Each compartment is sealed off by a membrane, just like a room has walls and a door. In fact, the metochondrion has four seperate sections. Counting everything, there are more than twenty different sections in each cell.

Cells are constantly getting rid of old stuff and manufacturing new components, and these components are designed to work in one room but not others. Most new components are made at a central location in the cell on things called ribosomes."

<Lee Strobel:>

Denton has described the ribosome, a collection of some fifty large molecules containing more than one million atoms, as an automated factory that can synthesize any protein that it is instructed to make by DNA. Given the correct genetic information, in fact, it can construct any protein-based biological machine, including another ribosome, regardless of the complexity. Denton marveled:

<Denton>

"It is astonishing to think that this remarkable piece of machinery, which possesses the ultimate capacity to construct every living thing that has ever existed on Earth, from a giant redwood to the human brain, can construct all its own components in a matter of minutes and... is of the order of several thousand million million times smaller than the smallest piece of functional machinery ever constructed by man."

<Behe again>

"Not only is the ribosome amazing, but now you're faced with the challange of getting these new components into the right rooms where they can operate. In order to do that you have to have another complicated system, just like you need a lot of things in place for a Greyhound bus to take someone from Philadelphia to Pittsburgh.

First of all, you've got to have molecular trucks, which are enclosed and have motors attached to them. You've got to be able to identify which components are supposed to go into which truck - after all, it doesn't do any good if you just grab any protein that comes along, because each one needs to go to a specific room. So there has to be a signal attached to the protein - sort of a ticket - to let the protein onto the right molecular truck. The truck has to know where it is going, which means having a signal on the truck itself and a complementary signal on the compartment where the truck is supposed to unload its cargo.

When the truck arrives where it's supposed to go, it's kind of like a big ocean liner that has crossed from London to New York. it pulls up at the dock and everyone's waving - but, oops, they forgot the gang plank. Now what are you going to do? You see, you've got to have a way for the cargo to get out of the truck and into the compartment, and it turns out this is an active process that involves other components recognizing each other, physically opening things up, and allowing the material to go inside.

So you've got numerous components, all of which have to be in place or nothing works. If you don't have the signal, if you don't have the truck, you'r pretty much out of luck. Now, does this microscopic transportation system sound like something that self-assembled by gradual modification over the years? I don't see how it could have been. To me, this has all the earmarks of being designed."

Strobel also quotes the documentary Unlocking the Mystery of Life:

In a process known as transcription, a molecular machine first unwinds a section of the DNA helix to expose the genetic instructions needed to assemble a specific protein molecule. Another machine then copies these instructions to form a molecule known as messenger RNA. When transcription is complete, teh slender RNA strand carries the genetic information... out of the cell nucleus. The messenger RNA strand is directed to a two-part molecular factory called a ribosome.... Inside the ribosome, a molecular assembly line builds a specifically sequence chain of amino acids. These amino acids are transported from other parts of the cell and then linked into chains often hundreds of units long. Their sequential arrangement determines the type of protein manufactured. When the chain is finished, it is moved from the ribosome to a barrel-shaped machine that helps fold it into the precise shape critical to its function. After the chain is folded into a protein, it is then released and shepherded by another molecular machine to the exact location where it is needed.

So what do we end up with? An incredibly complex system of complex and independant parts that function together to first, hold the recipe for a protein, second, take that recipe to a factory that will build the protein, third, build the protein, fourth, take the protein to the exact part of the cell where it is needed, and fifth, assemble the proteins into the necessary machine in a process which, though chemical affinities are a big part, cannot be replicated outside of the cell, and finally, the part must be put to use.

You list five steps. I don't agree with that. It's too simplistic. If we had to label steps we should label more than that. You could easily break it up into 50 or even 100 steps. But the individual steps don't show the need for design. The interactions do. This is an extremely complex process that does not lend itself to an evolutionary model.

And we haven't even gotten to the question of where the DNA came from.

[BGoodForGoodSake]

Of COURSE there are mechanisms within the cell that allow it to create proteins and assemble them into the various components that it needs. Affinities within the cell are a big part of that.

Now we are getting somewhere.

You agree that a cell has the ability to reproduce itself. That the mechanisms of protein formation are already in place.

We don't even need to discuss the origin of DNA nor the cell nor even life to discuss the origin of the flagellum.

Lets take a good look at the system.
Let's just imagine for a second that a mutation does occur during the reproduction process. One of the daughter cells has a change of DNA in one of it's genes.

What will happen?

You will get a different mRNA.

This will lead to a different amino acid chain.

And this will lead to a new protein.

Do you see a problem with this analysis?

Now can we predict how this new protein will interact with the rest of the complex chemical inteactions in the cell? No we cannot do it accurately due to the complexity of the cellular environment. But we do know that much of the time this new protein will cause impaiment, either by interfering with other processes or by the simple fact that a protein which was required no longer works as intended.

The cell is a product of the various proteins interactions. Sometimes a mutation leads to a breakdown.
Like in parkinsons disease.

We also know that in many cases nothing occurs. The protein simply gets lodged in the cell membrane and eventually within the gene pool it will be subject to additional mutations.

So what we need to look for now is a precursor system, something like the flagella but not exactly.

One clue is the fact that the flagellum is not necessary for survival.
This article touches on a few subjects. The study was done on a virulent bacteria and the function of the flagellum in its creation of a biofilm colony. In short the flagellum interfered with the strains virulence when in a host animal. The main focus of the study is the relation of virulence to the presence or absence of the flagellum.

Now I won't go into specific precursor systems in this post.

But what I have shown is how novel proteins can originate, due to the machinery of the cell.

[Wall-dog]

We don't even need to discuss the origin of DNA nor the cell nor even life to discuss the origin of the flagellum.

I'll give you that for the sake of this discussion, however you can't start with a flagellum either. I'm also going to hold that the other issues are related so while I'll grant that for this discussion you don't have to explain them I'm still going to feel free to discuss them as they relate to this discussion.

You agree that a cell has the ability to reproduce itself. That the mechanisms of protein formation are already in place.

I'll grant this statement but I'm not going to let you infer much from it without asking for evidence.

Let's just imagine for a second that a mutation does occur during the reproduction process. One of the daughter cells has a change of DNA in one of it's genes.

What will happen?

You will get a different mRNA.

This will lead to a different amino acid chain.

And this will lead to a new protein.

I won't deny that mutation does occur. As for evolution occuring because of it at the cellular level, I'll quote Dr. Behe again:

For most irreducibly complex systems, the best (darwinist explanation) you get is a sort of hand-waving, cartoonish explanation, but certainly nothing that approaches being realistic. Even evolutionary biologist Andrew Pomiankowski admitted: 'Pick up any biochemistry testbook, and you will find perhaps two or three references to evolution. Turn to one of these and you will be lucky to find anything better than 'evolution selects the fittest molecules for their biological function.'

But for the flagellum, there aren't even any cartoon explanations. The best Darwinists have been able to muster is to say that the flagellum has components that look like the components of other systems that don't have as many parts, so maybe somehow this other system had something to do with the flagellum. Nobody knows where this subsystem came from in the first place, or how or why the subsystem may have turned into a flagelllum. So, no, there's no reasoned explanation anyone has been able to offer.

One clue is the fact that the flagellum is not necessary for survival.
This article touches on a few subjects. The study was done on a virulent bacteria and the function of the flagellum in its creation of a biofilm colony. In short the flagellum interfered with the strains virulence when in a host animal. The main focus of the study is the relation of virulence to the presence or absence of the flagellum.

Could you please post the relevant part? This is what I found:

Taken together, these experiments suggest that some bacteria repress flagellar synthesis and increase exopolysaccharide synthesis in a biofilm and that these two functions may be co-ordinately regulated during biofilm development. Interestingly, for rugose V. cholerae O1 El Tor, wild-type levels of both motility and rugose exopolysaccharide depend on genes involved in the type II secretion of proteins (Ali et al., 2000). Thus, in V. cholerae O1 El Tor, rugose exopolysaccharide production and motility may have common steps in their regulatory and/or biosynthetic pathways.

As detailed above, there are several examples of bacteria that cease flagellum synthesis and initiate exopolysaccharide synthesis in a biofilm. The question remains, however, whether there is a regulatory relationship between the absence of flagellum synthesis and exopolysaccharide synthesis. The flagellum is involved in the regulation of other behavioural transitions such as the swimming to swarming transition of Vibrio parahaemolyticus and other organisms (Belas et al., 1986; Kawagishi et al., 1996). In this paper, we describe a role for the flagellar structure in the regulation of rugose polysaccharide biosynthesis by V. cholerae O139, and we show that increased production of rugose polysaccharide by flagellar mutants alters colony morphology, biofilm development and intestinal colonization.

Specifically:

The flagellum is involved in the regulation of other behavioural transitions such as the swimming to swarming transition of Vibrio parahaemolyticus and other organisms

That refutes you. Did you read the article before you posted a link? I would ask again that you quote the relevant part of your sources because I have a very hard time finding things in them that support your position.

Now I won't go into specific precursor systems in this post.

According to Dr. Behe, you can't go into specific precursor systems because there aren't any.

But what I have shown is how novel proteins can originate, due to the machinery of the cell.

Which, according to Dr. Behe, is something that has yet to evolve into a 'cartoonish explanation.'

Dr. Behe:

But the issue remains - can you use numerous, slight, successive modifications to get from those other functions to where we are?

[sandy_mcd]

Nowhere in your sources does it say anything about proteins assemblying themselves. It talks about the assembly occurring within the cell but it shows the rest of the cell as being an integral part of that process.

Could you please define what you mean by self-assembly? I have pointed out earlier that your use of a non-standard definition has caused a great deal of confusion and resulted in many unnecessary posts.
Google "protein self assembly" or look it up in a science database or Wikipedia. Note that your definition does not correspond to what most people mean.
Presumably you are referring to the formation of the primary structure of the protein which is the joining of specific amino acids to form the protein polymer. Note that this is not the standard definition. If you think it is hard trying to figure out what part of a link Bgood is referencing, try to imagine how difficult it is to understand what you are saying.
And if that is what you mean, no one here is saying that a bunch of amino acids show up at a party and do the conga on their own. Of course DNA etc are involved. I think everyone will agree with that part of your claim.

[aa118816]

I am not sure how evolution occured, but the process of NS plus RM is a quickly dying theory. The World Summit on Evolution severely cut down ND and had the top, not just the loudest, but the top evolutinary theorists debating replacement theories. Discussing NS+RM is almost like debating whether the steady state theory is viable.

Dan

[sandy_mcd]

We are talking about creating the flagellum. How did it initially come to be? How do you create a flagellum without the mechanism for creating it already in place? How does it come from other, less complex components?

Check out some of the specs on this:

# Precision ground ball screws, 0.0003" accuracy, 0.0001" repeatability
# Servo resolution 0.000025", no backlash

How is it possible that this mill can have an accuracy of 0.0003 inches and and even smaller servo resolution? What machine made this mill so that it can be so accurate? What had enough accuracy to make the machine that made the mill? Logically, it seems impossible, but we know this mill exists - you can purchase it.

We are talking about creating the milling machine. How did it initially come to be? How do you create a mill without the mechanism for creating it already in place? How does it come from other, less accurate and precise components? [Mere intelligence is not enough; I bet Einstein couldn't have made such a thing from scratch.]

[sandy_mcd]

Dr. Behe again:

But for the flagellum, there aren't even any cartoon explanations. ... So, no, there's no reasoned explanation anyone has been able to offer.

From Early Evolution, From the appearance of the first cell to the first modern organisms by Martino Rizotti, (c)2000 of the English edition, Birkhauser Verlag:
p53 4 Prokaryotes: The Flagellum
4.1 The bacterial flagellum is a complex structure
p56 4.2 Complex structures appear only once
p58 4.3 From what did the flagellum derive?
p59 4.4 Possible derivation series
ends on p62
Admittedly there is not much here, but it is more than the cartoon explanation which is alleged not to exist.

[BGoodForGoodSake]

Taken together, these experiments suggest that some bacteria repress flagellar synthesis and increase exopolysaccharide synthesis in a biofilm and that these two functions may be co-ordinately regulated during biofilm development. Interestingly, for rugose V. cholerae O1 El Tor, wild-type levels of both motility and rugose exopolysaccharide depend on genes involved in the type II secretion of proteins (Ali et al., 2000). Thus, in V. cholerae O1 El Tor, rugose exopolysaccharide production and motility may have common steps in their regulatory and/or biosynthetic pathways.

Let me translate for you. Exopolysaccharide are sugar molecules which are ejected from the cell. They are stating that an inverse relationship between flagellum formation and sugar secretion exists. In other words they may use the same mechanism.

As detailed above, there are several examples of bacteria that cease flagellum synthesis and initiate exopolysaccharide synthesis in a biofilm. The question remains, however, whether there is a regulatory relationship between the absence of flagellum synthesis and exopolysaccharide synthesis. The flagellum is involved in the regulation of other behavioural transitions such as the swimming to swarming transition of Vibrio parahaemolyticus and other organisms (Belas et al., 1986; Kawagishi et al., 1996). In this paper, we describe a role for the flagellar structure in the regulation of rugose polysaccharide biosynthesis by V. cholerae O139, and we show that increased production of rugose polysaccharide by flagellar mutants alters colony morphology, biofilm development and intestinal colonization.

A biofilm allows bacteria to stick to and group together at surfaces. There are several examples of bacteria which stop producing their flagellums and instead excrete sugar molecules. What they want to uncover is whether there is a relationship between flagellum formation and sugar excretion. The paper examines the role of the flaggellum system in this excretion process. Through experiments they show mutant forms, (those without flagellums) increased their excretions and also had other effects on how they bunch together.

The flagellum is involved in the regulation of other behavioural transitions such as the swimming to swarming transition of Vibrio parahaemolyticus and other organisms

You took this out of context, this is an introductory sentence. It states that we know the flagellum in involved in transition from moving to swarming from another study. But we will go further into the function and mechanism of the flagellum in some species of bacteria. And find out how the flagellum is involved in more detail.

The flagellum is involved in the regulation of other behavioural transitions such as the swimming to swarming transition of Vibrio parahaemolyticus and other organisms (Belas et al., 1986; Kawagishi et al., 1996). In this paper, we describe a role for the flagellar structure in the regulation of rugose polysaccharide biosynthesis by V. cholerae O139, and we show that increased production of rugose polysaccharide by flagellar mutants alters colony morphology, biofilm development and intestinal colonization.

That refutes you.

It does?
How?
lol

Did you read the article before you posted a link? I would ask again that you quote the relevant part of your sources because I have a very hard time finding things in them that support your position.

there is evidence that flagellum and exopolysaccharide synthesis are inversely regulated

Meaning the sames tructure may be involved in both functions.

Taken together, these experiments suggest that some bacteria repress flagellar synthesis and increase exopolysaccharide synthesis in a biofilm and that these two functions may be co-ordinately regulated during biofilm development.

Experimentation both through analysis of naturally occuring mutants and mutants formed by knocking out genes showed that both functions are related.

Because the rugose colony morphology has been correlated with exopolysaccharide production, this suggested to us that increased exopolysaccharide synthesis in V. cholerae O139 was somehow dependent on the flagellar structure

Both functions depend on the same structure.

[sandy_mcd]

Think about it in terms of me giving you two buckets of compounds. Call compound one 'A' and compound two 'B'. Let us further suppose that these two compounds have a chemical affinity for one another. Now we dump them into a bug tub together. What will happen? They will begin to bond, but they will not bond in irregular patterns because B does not bond to B and A does not bond to A so I'll always get patterns of ABABABABABABAB and so on. You'll have to forgive me for making it a one-dimensional pattern. In real life it would be three-dimensional. But I think you get the picture. That is self assembly and as Dr. Meyer shows, self-assembly always creates patterns. You never get irregularities. Also, self-assembly would require no DNA as the chemicals would assemble themselves without it. This is how crystals form but I would ask you to look at the protein you posted and ask yourself if it makes sense to think that chemical affinities create that kind of an irregular makeup. Self-assembly always creates regular patterns.

Ah, I now see where you are getting your (mis)information from. http://www.geocities.com/lauho08/eviden ... eator.html is a selection from Lee Strobel's "The Case for a Creator". You are primarily referring to SCENARIO #3: CHEMICAL AFFINITIES AND SELF-ORDERING. This topic is pretty much peripheral to whatever the theme of this thread is but you have unfortunately wandered into an area I profess to know at least a little about.
1) You are mixing up chemical reactions and/or molecular conformation with crystal structures. I have no idea what you are trying to say unless you give some more specific examples of what A and B might be.
2) Your statement about never getting irregularities shows you have no experience with the real world. Chemical reactions and crystals are full of irregularities. It is only in textbooks that things work out so nicely.
3) Looking back to the protein picture I posted, of course the structure is due to chemical affinities. Ignoring larger proteins which need chaperones, how else is the three dimensional structure generated if not by chemical affinities?
4) Ultimately, none of this is relevant. I (and presumably Bgood) are willing to stipulate almost all of what you have said about protein formation (read Bgood's posst for a more detailed explanation). You look at a complex set of circumstances and conclude intelligent intervention is necessary whereas I look at the same and don't see the need. Just because I can't understand it is not for me sufficient reason to invoke other explanations.

[Canuckster1127]

I'm almost afraid to chime in here.

First, I've read this thread and tried to understand it. I have to confess, my eyes are glazed somewhat and this is not my field of expertise and I'm impressed at the level of detail that is present here.

I am familiar with the idea of irreducible complexity as put forth by Behe and it obviously is a subject that requires more understanding and specialized training than I possess to interact here.

My concern is this, and it will necessarily have to be at a simpler level than what you are doing here, which again impressed me.

My concern is that Behe's argument, at its root is essentially another form of the old "God of the Gaps" argument. It in essence, states that because we cannot explain through natural means, why something is the way it is, it must therefore infer that there is a creative power and intelligence behind it and further it leaps to the next plateau which is to state that not only is that intelligence necessary, it must have intervened in some manner to supersede that which is possible by chance and solely naturalistic means.

My concern is that this "line in the sand" stating irreducible complexity will fare no better than such past assertions that have in the past been disproven or better explained over time.

If and when that happens, then we give those in opposition to us on this count, the club to beat us. Seems we don't learn.

Don't misunderstand, I am a creationist and I believe God authored and designed this world and all it components. I think inference is a reasonable means to arrive at that conclusion, although I believe it ultimately by itself is insufficient. I just don't like seeing us make the same mistakes repeatedly by presuming that because there are not answers now, that there will not be answers as knowledge expands.

We're not seeing the forest for the trees.